Threads I Unravelled
by theicemenace
Summary: John Sheppard loses his ability to control Ancient technology leaving his job, and his life, in jeopardy. It's up to his Atlantis family to figure out what went wrong and fix it. Shepp/McKay whumpage.
1. Following a Pattern

**A/N:** Many thanks to my friend ladygris who encouraged me to write something a little different from my usual fluffy fare. She also Beta'd and brainstormed. DaniWilder also gave me a few ideas.

Thanks to both,

~ Sandy ~

**Threads**

**Chapter 1**

**Following a Pattern**

The wormhole shot out of the center of the Stargate on the planet designated M7M-536 and seconds later a Jumper emerged banking around to land nearby. A squad of Marines was left to guard their only way off the planet then the Jumper lifted off again to head toward the sun. Inside, the members of Team Sheppard were each engaged in their own pursuits. Teyla tapped at her PDA while Ronon closed his eyes, his long legs blocking the aisle. In the shotgun seat, Rodney had his computer out analyzing the MALP data while John did what he did best, flew the Jumper.

They flew in silence for a while, but John could only take it so long. "So, Rodney, you and Keller have a date tonight?"

The physicist answered without bothering to stop what he was doing. "If it's any business of yours, which it's not, yes. We're going to movie night." He looked up sharply when his friend snorted. "What?"

"Nothing." John tried to look innocent but he could never pull it off. "It's just that _Aliens_ is the movie tonight."

"But Jennifer told me it was _How to Lose a Guy in Ten Days_."

"Maybe we're both wrong." The Colonel snorted, obviously pulling Rodney's chain. "How'd she convince you to go anyway?"

Rodney looked at John and away. "She's a, uh, Matthew McConaughey fan."

Teyla took her nose out of her hand-held and smirked. "I have seen several movies with this Matthew McConaughey. He is very handsome, especially when he takes his shirt off, and speaks with an unusual accent that I find very…appealing."

Ignoring his companions, Rodney turned back to the front window. "We should be coming up on it just about…" he raised his hand and pointed, "…now."

A building came into view and even though it was nearly invisible from the overgrowth of plant life, they could tell it was Wraith design. The difference here was that it didn't look like a ship that had been turned into a ground-based laboratory. It had the mark of being a permanent structure.

"Rodney?"

"It's just as we thought. There's minimal power and the signature suggests there might be a ZedPM somewhere on the premises."

Now that there was a real chance that he'd be able to kill Wraith, Ronon was awake and attentive. "Teyla?"

"I do not sense any Wraith, but we are still far away."

"Rodney? Any life signs?"

More tapping at the computer. "Hard to tell at this distance, but judging by the encroachment of flora and fauna, I'm gonna go with no."

~~O~~

John did a quick flyover and landed near the main entrance. The team disembarked and cautiously approached the front of the building. When they got close Rodney raised his hand. "Wait." The others watched the surrounding foliage warily while he stared at his scanner.

"What d'you see?"

"Huh? Oh, nothing. I was gonna sneeze." Rodney took out a bottle of water and used it to swallow a pill just as John reached out to slap him on the back of the head. "I can't help it if I have _allergies_." Rodney went to the door, pulled dark green ivy tendrils out of his way and touched the controls in what looked like a random pattern. It slid open with a grinding noise that spoke of hundreds, maybe thousands, of years of disuse.

Flicking on the lights from their P-90's, John took point with Rodney just behind him and Teyla and Ronon on their six. They followed Rodney's directions turning left and right when told to until they came to a large open area surrounded by stasis chambers and what looked like cabinets. The air smelled stale though there was the slight hum of an air filtration system, almost as if it were just a background noise you could easily ignore. Dust and other unidentifiable substances were in piles all over the floor. The clincher that this was a Wraith facility came when John located a pile of desiccated corpses in a far corner. He gave them a moment of empathy and moved on.

"This looks like one of Michael's labs."

"Too old for that though it _is_ a medical lab of some sort. Touch _nothing_." Rodney aimed that last at John as he unhooked his P-90 and set it aside. He attached his computer to the main console in the center of the room, manipulated the controls and the lights came on.

As Rodney downloaded the database John roamed around opening hatches and trying to peer into stasis chambers. All were empty. He came to a small alcove that had two circular pads on the floor and in the ceiling like a miniature transporter. It was just big enough for two people to stand side by side. A keypad began to flash. "Hey, Rodney…"

In a distracted tone, the physicist said, "In a minute. I just need to…" His voice trailed off.

"But it's…"

John reached out with a finger to touch the keypad when it began to flash faster just as Rodney rushed forward shouting, "No, _don't!_"

Just as he grabbed John's arm, a light came down from the pads in the ceiling pinning both men in place. They stiffened, held fast, the sounds of Teyla and Ronon calling their names fading away.

~~O~~

John's vision darkened as every muscle in his body felt as if it were being pulled in ten different directions, none of them the way they were meant to go. The forefinger of his right hand spasmed repeatedly on the trigger of his weapon and he was thankful that the safety was on. He heard his name being shouted again as his jaw clenched. Moments later, the light shut off and John slumped unconscious into Ronon's arms.

~~O~~

Rodney watched silently as John writhed in pain though _he_ only felt a warm and gentle pushing sensation. Dizziness assailed him then just as suddenly was gone when the light winked out. He staggered and Teyla was there to keep him from falling.

The Satedan lowered John to the floor while Teyla, after making sure Rodney was okay, unhooked the neck strap and pried the P-90 from his hand. "John!" She lightly slapped him on the cheek but he didn't respond. Pressing her fingers under his jaw, she was relieved to feel his pulse steady if a little weak. The muscles in his arms, legs and rib cage were still contracted pulling him into a fetal position and causing him to breathe shallowly.

Rodney had left his computer to complete the download on its own when he attempted to stop John from touching the keypad. Now he knelt down next to his friend. "How is he?"

"Unconscious but uninjured as far as I can tell. We must get him back to Atlantis."

A beep from his computer sent Rodney scurrying back to the console. As he disconnected his computer John groaned. With Teyla and Ronon's help he was able to sit up.

"How do you feel?" Teyla's dark eyes were filled with concern.

John did a quick self-diagnostic and didn't like the result. "Like, uh…"

"…crap?" Teyla provided with a lift of one eyebrow.

"I was gonna go for something stronger, but that'll work. You guys okay?"

"We are fine. Can you stand?"

"Yeah." Teyla stepped back while Ronon lifted John to his feet with little effort. John's knees buckled and only Ronon's hands under his arms kept him from landing face first on the dirty floor. "No." He groaned again. "What happened?"

"You activated _that_ device, whatever it is." Rodney answered from across the room. "Exactly which part of '_touch_ _nothing'_ is so difficult for you to understand?"

"Sorry." The strength slowly seeped back into his extremities and this time when Ronon let go, John was able to stay standing. The LSD clattered to the floor when his left hand finally unclenched.

"Sorry?" Rodney's voice rose to a screech on the end. "How does 'sorry' help? Have you forgotten any of a hundred other alien devices that have had detrimental effects on the person or persons unlucky enough to be in the vicinity of one of your 'sorries'? And this time, you managed to take _me_ with you on some weird journey to God knows where. This had better not be another ascension machine because I am _not_ in the mood to release my burden. I want to stay good and _pissed off_ for the foreseeable future."

"Rodney," Teyla admonished the physicist as she retrieved the LSD from where it had fallen and returned it to John.

The Colonel glanced down at the device in his hand but the screen was blank. "Oops." He tucked it inside his vest with a shrug.

"Perfect." Rodney's tone indicated otherwise. "I suppose you want me to _fix_ that too."

"If it wouldn't be too much trouble." John's voice was stronger now and he was able to move on his own. Every muscle ached as he stretched and massaged his arms and legs.

"While it is a _major_ imposition, it's also my _job_. Just…bring it to the lab and I'll get to it sooner or later." Rodney was huffing and complaining under his breath, his companions ignoring his mumblings as they always did. "Probably later."

"Gee, _thanks_." John said with sarcasm certain he'd never get the thing back. He walked around the room working the remaining knots of rigidity from his muscles though there was one spot in the middle of his back he wasn't able to reach.

"We done here?" Ronon asked ready to go now that he knew there were no Wraith to kill.

Coming to his feet, Rodney completed the shutdown of his computer and stowed it in his backpack. Shrugging the straps up over his shoulders, he headed for the exit. "Now that Colonel McGoof-up is able to walk on his own, yeah. Let's get back to Atlantis. I'll put Zelenka to work analyzing the data while we get our post-mission physicals."

"And…" John asked as they headed down the first corridor.

"_And_ I'll fix your LSD as soon as I'm absolutely certain I'm not going to mutate into some heretofore unknown species with phenomenal cosmic powers and an itty-bitty living space." Rodney took out his scanner and brought up the schematic he'd located in the lab's computer. "That way."

~~O~~

On the way back to the Jumper, John stopped to rub his back on a tree. His skin was beginning to itch as if thousands of insects were crawling on him. His companions watched him, Teyla with concern, Ronon impassively and Rodney with disdain.

"Whenever Yogi's done showing us what bears _really_ do in the woods, we should get back to Atlantis."

The Jumper's hatch opened when Rodney hit the remote and the team took their usual seats. John joined them a few seconds later still trying to scratch his back. He settled into the pilot's seat, tucking his P-90 out of the way. When he touched the controls his eyebrows came together in puzzlement. _What the hell?_ He removed his hands and tried again.

"We can _leave_ now." Rodney prodded.

"I'm _trying._ It's _not_ _working_."

Rodney gestured him away from the controls. "What did you _do_ to it this time?"

"_Nothing_. It was working when we landed."

Teyla leaned forward in her seat. "There are no Wraith here. Could you have missed a life form that may have damaged the ship?"

"I didn't miss any_thing_ or any_one_." Taking John's seat, he touched the controls experimentally and it immediately powered up. "It's working now." He traded with John again and the power levels dropped to zero once more. With a huff of annoyance, the physicist leaned past his friend, one hand resting on the edge of the console. The power came up again startling both men. It also got Rodney to thinking and he didn't like the path his thoughts were taking but once started, they continued on to a logical, disturbing conclusion. "Uh-oh."

"You said uh-oh, Rodney. _Why_ did you say uh-oh? Nothing good _ever_ comes after _you_ say 'uh-oh'." John reminded him with more than a little apprehension.

Rodney ignored him snapping his fingers. "Let me see the LSD. The one you _supposedly_ broke."

"Supposedly?" John pulled the device out of his vest pocket and passed it over. "It's _fried_. Why…" He stopped talking when the device lit up the second it touched Rodney's hand. "What the…" Snatching it back, the bad feeling he already had increased when it went dark again. "_Rodney_?"

"I'm not a medical doctor, as you well know, but if I had to guess, it looks like…"

"What? It _looks_ like _what_?" John had an idea what had happened but needed to have it confirmed by someone other than himself and Rodney was as good a someone as anyone until they returned home.

"Whatever that thing was that we were hit by when I told you _touch nothing_…it's affected your ATA gene." Rodney's pronouncement left them all stunned as his eyes met and held John's.

Ronon cleared his throat. "Isn't this were you say…"

Together, John and Rodney said, "Oh, _CRAP!_"

**TBC**


	2. A Life Unraveling

**A/N:** Many thanks to ladygris who encouraged me to write something a little different from my usual fluffy fare. She also Beta'd, brainstormed and helped with ideas.

Thanks also go out to dwparsnip for the use of an element from one of his stories. He knows which one it is. ^_^

~ Sandy ~

**Threads**

**Chapter 2**

**A Life Unraveling**

"_This_ is a _disaster_!" Rodney continued alone.

"Duh." John huffed at him. "_What_ was your first friggin' _clue_?"

"Other than not being able to fly the ship, how do you feel?" Teyla asked concerned for her friend's welfare.

"I _feel_ _fine_." John looked at the faces of his friends seeing what he thought was pity in their eyes. "I'm sure it's just a temporary thing. It'll be back to normal in the morning. Right, Rodney?" The physicist stayed silent. "Rodney?"

"I have no idea. I mean, w-we have no idea what the intended purpose of that machine was. _Maybe_ it's transitory. Maybe not." Rodney sighed heavily. "Let's just get back to Atlantis and thank the IOA for creating the rule that said there should be at least two people with the gene on each team or we'd be in it hip deep right now."

John thought about everything Rodney said realizing he was right. "Sure. Sorry." He exchanged a sad smile of remorse with Teyla, and Ronon shrugged. Turning to look at the co-pilot's seat, he gave it a look that said he'd rather be left alone with a hungry Wraith than sit there. He slid into the seat as Rodney powered up and lifted off.

On the way to the Stargate, Rodney bore John's side-seat driving without comment, for the most part. As they neared the open field surrounding the Stargate, John came to stand over him, one hand on the back of his seat and the other on the console. "Be _careful_, McKay. The space between those trees is kind of tricky. You have to tilt to the left and…no-no-no! You're coming in too steep! Angle the nose up about ten degrees and…"

"_Obviously_ I'm not doing this right. Would _you_ like to drive? Oh, wait. You _can't_. So why don't you…"

"Rodney." Teyla's tone was a warning, one the physicist had learned to heed a long time ago.

"…have a _seat_ and we'll be just…_fine_." Rodney's teeth were clenched with the effort to control his temper, but he couldn't keep the sharpness from his voice. The remainder of the trip was taken in a strained silence. He landed long enough to pick up the squad of Marines left to guard the 'gate then circled around for the approach vector. "I usually do this but…"

"Oh, please let _me_ dial the 'gate, Rodney." John was being caustic and mocking and Rodney responded in kind.

"Why, John, it is _so_ _kind_ of you to offer. Please do."

While the displaced Air Force officer dialed home, one of the Marines, Gunnery Sergeant Brackman, came forward to ask Teyla, "What's _that_ all about?"

"It is a long story, Gunny. Perhaps you should read the mission reports once they are completed. I don't believe I could do it justice."

The Sergeant snorted in amusement though he wasn't sure if that was the proper response. "If you say so, ma'am."

The big Marine turned to the rest of his squad with a shrug. He regained his seat just as they entered the wormhole thinking he didn't know what the fuss was all about. McKay flew very well, almost instinctively. He made a note to speak to him later.

~~O~~

Jennifer and Carson were in the lab silently working side by side. They knew each other so well they seldom needed to speak except to draw attention to an interesting bit of information gleaned from their respective researches. And when they did speak, it was in verbal shorthand that few understood. Amanda was one of those valiant few who'd managed to break the code though she'd never tell them. She let them think they were enigmas to the rest of the staff.

Carrying a tray with a rack of blood-filled tubes into the lab she passed it over to the tech on duty then just as quietly left the room. She went to check on her patients, carefully charting their progress in the computer as she went.

That completed, she was just about to tell Jennifer she was taking a break when Team Sheppard and their Marine guards entered the Infirmary, Sheppard leading the way. They came to a stop in front of her, their weapons, TAC vests and packs absent having already been returned to the armory.

~~O~~

John resisted rolling his eyes at the amused glint in Amanda's eyes. It would only fuel her enjoyment of his predicament, whatever the outcome. They'd known each other since Stanford before she went on to Johns Hopkins and had always treated him as if his every move and thought were an open book to her. It annoyed him to no end though he wasn't sure why.

She looked him up and down with a grin. "Colonel John Sheppard and his team coming to the Infirmary for their post-mission physicals without being threatened? This is a momentous occasion." Crossing her arms, the doctor added, "So what planet did you find the flying pigs on?"

Stifled snorts came from the Marines, but John ignored them though he did harbor a momentary fantasy that had them all pulling duty in the waste treatment plant for the remainder of their tours. "We had an…incident on the mission. McKay and I need to have full physicals, blood, scanner, stress tests, the _works_."

Amanda's entire demeanor changed from friendly bantering to that of the consummate professional they all knew her to be. "Sorry, Colonel. I'll get Doctor's Keller and Beckett."

~~O~~

Jennifer went straight to Rodney's side gathering him into a hug. "Are you alright?"

"Yeah. Well, maybe. We, uh, got hit by some strange beam and John passed out." He let her step out of his embrace as she morphed from the woman who loved him into the Chief Medical Officer.

"Okay, you all know the drill." She, Carson and Amanda rattled off a long list of tests to be done while the Marines, Ronon and Teyla took their places at empty exam tables. John and Rodney were led to the private exam area where they were ordered to strip down and get into the semi-private gowns on the foot of the bed.

The phlebotomist came and took several vials of blood from the men then departed. She was replaced by another technician who gave them each several specimen collection containers after writing on the sides their names and type of specimen that should go in each. Not surprisingly, both men had the same reaction to one of the requests. Urine, blood, skin, hair, nails and saliva they could understand, but when it came to providing the final sample, they both balked.

Jennifer quickly put a stop to Rodney's stuttering complaints by taking him by the hand and leading him into her office. The door shut behind them and everyone wisely ignored what was more than likely going on behind it.

John, on the other hand, emphatically and categorically refused to provide a sample. The tech didn't say anything, just pursed her lips in irritation and walked away leaving the Colonel looking and feeling triumphant, but he wasn't allowed to enjoy it for long. The woman returned shortly with Amanda at her side.

The doctor pierced John with her hazel eyes filled with humor over his discomfort. "You said, and I quote, 'the works.' This is part of _the works_."

He thought about using his infamous death glare on her however, she'd never fallen for it in the past so it was pointless to waste it on her now. He waited while she disconnected his EKG and EEG monitors then headed for the bathroom. Just before the door closed, she held out the specimen cup topped with a green lid. "Let me know if you need someone to…give you a hand." Scowling, he snatched the container from her hand and went into the bathroom. She shook her head ruefully as the door slid shut on what sounded like "cod, ham, cheese and rice" but knew better.

When John finally emerged from the bathroom, Rodney was already in bed and wired up. Amanda reconnected John to the monitors and ordered him into bed. The two men avoided looking at each other as much as possible while technicians came and went performing all sorts of tests.

Eventually, each was taken to be scanned and to do a treadmill test. As a reward for being such good sports about everything, they were given dinner. Jennifer had a meal brought in as well and sat with Rodney.

~~O~~

Along with the burger and fries John had requested for dinner, there was a bottle of blue liquid in place of his usual iced tea. "What's this?"

The nurse rolled the table over his bed speaking as she did a quick check of his vitals. "Doctor's orders. Your electrolytes are out of balance. We also have it in green, red and orange."

With a shrug, John cracked the bottle open and drank down half of it before digging into his meal.

~~O~~

After he'd eaten, John demanded his computer from his quarters. Just to shut him up, Amanda went and got it herself. When she returned, she pulled a chair up next to his bed and took notes while he told her what happened in the Wraith lab. She was interested in how he'd felt physically at the time, but she also wanted to know about his mental state. Convincing him to talk about his emotions was even harder than getting him to provide that one sample. By being persistent and teasing, she was finally able to get him to admit that he'd been alarmed during the process. He also confided that finding out his ATA gene had stopped working scared him even more.

Amanda saved the information and pushed the keyboard away just as a technician motioned to her with a nod of her head. The two women conferred quietly and though she fought the urge to express shock at what she was being told, some of it must have shown on her face.

"What is it?" John didn't like being out of the loop and tossed back the covers to follow when she abruptly left in the direction of the lab. He'd only gotten one foot on the floor when the biggest Marine he'd ever seen pulled the curtain aside.

"'Fraid I'm gonna have to ask you to get back in bed, sir."

"But I'm…"

"My CO? Yeah, but I'm more afraid of _her_…" he tossed a thumb over his shoulder in the direction Amanda had gone, "…than I am of whatever _you_ might do to me."

John didn't have an argument for that so he just got back into bed.

A few minutes later Amanda returned. She whispered to Jennifer who got up and left Rodney's side without saying good-bye. Not long thereafter, Carson hurried past without greeting either of the men.

"What's going on?" Rodney asked and John looked at him for the first time in hours.

"Don't know, but my Spidey-sense is tingling."

Rodney's eyes widening with just a little fear. "Oohh, that's not good."

There was a long pause then, "Rodney…"

"On it." Putting his tray to the side, Rodney opened his laptop.

~~O~~

Amanda followed the lab tech into the main work area where she brought up the results of one of the tests they'd done on the two men.

"You double checked the results?" Amanda twisted a lock of her shoulder length hair trying to keep calm. It never helped, but she did it anyway.

The technician huffed in frustration. "We _quadruple_ checked the results."

"_Damn_. Bring up the other one."

The screen changed. "Better than normal. More plentiful and more active. Not as many dead."

Amanda touched her on the arm. "Sorry if it seemed like I didn't believe you. I'll get Carson and Jennifer."

~~O~~

John was standing next to Rodney's bed looking at the laptop monitor, his forehead creased in bewilderment. Displayed in front of them were the results of one of the tests. "You're sure _this_ is what they're looking at _right now_?"

"_Yes_." Rodney watched John from the corner of his eye waiting for some sort of response besides the nothing he'd gotten so far. "You okay?"

"Hell _no_ I'm not okay!" He paced as much as he could between the two beds. "Why wasn't I told about this before?"

Rodney waved a hand helplessly, the teasing attitude long gone. "Maybe _this_…" he pointed at the screen, "…is what that machine was supposed to do."

"Well, that _sucks_. Not that I was thinking of doing it anytime soon, but, you know, some day. Um, what about…"

"I _don't_ want to know." John gave him a pained look. "Fine. _There._" Rodney and John both peered at the monitor. The physicist crossed his arms and looked smug. "Happy now?"

"Not really."

John ran a hand through his unruly hair. "You know, that still doesn't explain why I wasn't able to use the LSD or fly the Jumper."

Rodney shrugged and drummed his fingers on the table waiting for his friend to speak again, watching his face carefully to gauge his reaction. "If you need someone to talk to…"

"Thanks for the offer." John gave Rodney's shoulder a squeeze.

"Actually, I was going to say you should call the staff shrink."

"Oh, right." Rubbing the back of his neck, John was about to return to his bed when Amanda entered. He didn't bother to turn his back so she was greeted with the seat of his boxers and waited for a snarky comment about his lack of modesty. He became concerned when she said nothing. "What's up?"

"Get dressed and come to my office, Colonel." She shut off his monitor and removed his EKG and EEG leads. "We have to talk."

Jennifer came in behind her with the same grim expression. "Rodney…"

"Private talk?"

"Yeah."

Jennifer removed Rodney's monitors and he and John watched the women walk away, exchanging an uneasy glance. "Think they know?" John asked but the physicist was already shaking his head.

"There's something else."

**TBC**


	3. The Ties That Bind

**A/N:** Many thanks to ladygris who encouraged me to write something a little different from my usual fluffy fare. She also Beta'd and brainstormed, coming up with some great ideas. Oh, and the title of this chapter was taken from the Erma Bombeck book of a similar title. I would have asked permission to use it, but she passed away April 22, 1996 from kidney disease.

LG helped with some of the dialog.

Thanks,

~ Sandy ~

**Threads**

**Chapter 3**

**The Ties That Bind**

Amanda looked up when she heard a light tap on her door. She gestured John to a chair and folded her hands together on top of the desk. "John, there was an anomaly in one of your tests." John had on his unreadable expression. She'd never liked that look because she couldn't tell what he was thinking. "We've, uh, done this one before, but only to have a baseline for comparison." With a sigh, she told him, "Even considering some of the things that have happened to you the last few years, we didn't expect this."

"What, uh…"

"We haven't done this test since just before you came to Pegasus and it was normal at that time. We're not sure what caused the current results though it might be reasonable to assume it was your most recent adventure or even a combination of your adventures." Amanda took a drink from a bottle of water then set it aside. "This is harder than I thought it would be. I-I've never had to give a friend bad news before. Not _this_ bad." She turned the tablet around and called up the test in question. "As you can see, most of…well, your, uh…you can't…you won't be able to…"

"Mandy, are you trying to tell me my swimmers can no longer do the backstroke?" Reluctantly, she nodded, her eyes dropping to the desk. Her head came up sharply when he sighed heavily in relief. "Thank _God_."

Concern for her friend turned to confusion. "John, you _do_ know this means you won't ever be able to have children, right?"

John nodded. "Already knew that. I thought you were gonna tell me I'm _dying_." He obviously wasn't happy about it but it was better than the alternative.

"But how…"

"Rodney hacked into the…um…" he made a sheepish shrug and wouldn't meet her eyes, "…good guess?"

"John." Amanda made her tone reproving. "There's something else…" She gave him a rundown on the other issues watching him just nod, not saying another word for the remainder of his time with her. When he was gone, she tapped her headset. "Cole to Keller. We have a mouse in the cheese."

~~O~~

Rodney sat down in front of Jennifer's desk and she took the chair next to him. He didn't know what to think because in _his_ world "private talk" meant the same thing as "red means bad."

"That test you didn't want to do that I helped you with?" She picked up her tablet from the desk and turned it so he could see the image on the screen. "This is not…normal. There's more than twice the number of sperm in this sample than average."

"Always knew I was above average. This just confirms it." He couldn't keep self-satisfaction from his voice. "When we're ready to have kids…"

"But we're _not_. At least not yet. The last time you had this test it was average. Exactly average. And this, well _this_ is way, _way_ above average." She took him by the hand. "We'll have to use additional protection when we, um, because yours are so…active, they might, well, just in case."

The smug grin that had been on Rodney's face since he and John had hacked into their medical charts disappeared when he realized that Jennifer wasn't kidding. "And that's not good?"

"No, honey, it's not."

"Okay. So we use extra protection. No big deal. We done here? 'Cause I really should…"

Jennifer's hand on his arm stopped him from leaving. "There's something else." She tapped the screen on the tablet and brought up another image. "This is DNA."

"Uh, yeah, I know."

"It's _your_ DNA. See this?" She pointed to a particular area on the monitor. "It means that your ATA gene is natural, not artificially induced."

"I didn't know that was possible." He could hear the excitement in his own voice and cleared his throat.

"It isn't. What we, Carson, Amanda and I, think happened is…"

~~O~~

John hadn't left the Infirmary yet by the time Rodney came out of Jennifer's office. They didn't say anything to each other just headed for the exit. The moment before they'd have been home free Carson, Jennifer and Amanda came out of the lab and their offices respectively. And they looked _pissed_.

Jennifer crossed her arms and glared at the man she loved carefully enunciating each name. "Meredith. Rodney. _McKay_."

"Uh-oh," was all Rodney said.

"You know I don't like it when you say 'uh-oh', right?" John said out the side of his mouth.

"Yeah."

"Just checkin'."

"You _hacked_ the medical database. That is lower than low." Jennifer's brown eyes had changed to a reddish color as they did when she was way beyond just being a little ticked off.

John came to his friend's defense. "It was _my_ idea."

"He didn't have to go along with it."

"True." Rodney huffed at him. "Well, it _is_."

Jennifer eased her angry stance. "Since you only looked at yours and John's charts, I'm gonna let it go without reporting it to…"

"The military commander?" At her sheepish grin, John gave her a grin back then left the Infirmary. When they were out of sight of the Infirmary entrance, the two men parted, Rodney to his lab and John…he went out on the balcony and just watched the moons. One was full and at its apogee. The other was a crescent and several days off its perigee.

He tapped his right heel on the deck restlessly wanting to run and keep running. Run so far and so fast that he could outrun what was going on inside his body. Or rather what was _not _going on. For years he'd put off having a long-term relationship with a woman beyond business, friendship or the transitory and now who would want him? He was…damaged, unable to father children. And the one thing he could have passed on to those children, the one thing that made him _special,_ was gone. Without either, he was nothing but a career soldier who got lucky on more than a few occasions, the most recent when he sat in a strange chair that had looked like a recliner but was infinitely more.

He was still staring out at the water hundreds of meters below when he received a call advising him of a meeting in the main conference room. Without asking he knew what would be the subject-_subjects_ of discussion. Pushing down his first instinct, to refuse to answer, he made his way to Operations.

~~O~~

Woolsey, Jennifer, John, Carson, Amanda, Evan, Radek, Ronon and Teyla, were already seated in the conference room when Rodney arrived, their faces unsmiling. He hadn't meant to arrive late but after he and Jennifer had talked he'd gone for a long aimless walk and ended up in an area of the city with no transporter and had to walk all the way back.

The last time he was this embarrassed was in grade eight when he'd been pantsed in front of the girls' soccer team as they did practice drills on the field. What Jennifer had told him was embarrassing in the extreme though it hadn't been his fault. He could only imagine how John felt.

After orbiting the room until he reached the chair across from John, he realized that they'd have to look at each other so he changed his mind. He'd rather sit next to him where he didn't have to look at him. Circling back around, he took the one beside the man who was, thanks to the Wraith, now more than just a friend, at least according to medical tests. "Was this _your_ idea?"

"No. It was _theirs_." John nodded at Jennifer and Amanda.

Rodney muttered an oath under his breath and waited for it all to begin so it would be over.

~~O~~

"…the physicals for the Marine squad, Ronon and Teyla all came out normal with the standard exams. By their own admission, McKay and Sheppard were the only ones affected by the Wraith device, so, at the Colonel's request, they got the complete physical. All the bells and whistles." Jennifer was standing alongside the large monitor, remote in hand. "And I do mean _all_."

John shifted in his chair. "I haven't had a physical _that_ thorough since I returned from Afghanistan."

"We would've ended up doing the tests anyway based on the results of the others." Jennifer indicated the others in the room. "You guys sure you want to do this?"

_No! _John nodded unenthusiastically. "Yeah."

_Hell no!_ Rodney flushed to the roots of his hair. "If you must."

Jennifer reddened as well, taking a deep breath in an attempt to dispel the nervousness. "Okay. Here goes…" She pressed the remote and brought up what was obviously a semen sample. Most of the little guys were just lying there and the few that were moving did so sluggishly. All were grotesquely misshapen, a few had stunted tails. "As you can see, the majority of the spermatozoa are dead, but even if they were living, they would be unable to fertilize an ovum because the nuclei are severely damaged." They watched as some of those that were still motile ceased wiggling. She kept her gazed averted from John's face. "As you were told, Colonel, it means that you'll never be able to father a child." Jennifer pointed her chin at the monitor. She didn't like giving bad news and this was just the beginning. "If you can't father children, you can't pass on the gene that allows you to control Ancient technology. We'll touch on that subject again in a few minutes."

Another click and a new image came up on the monitor. In this one, the sperm were much more plentiful and _very_ active. "Normally, there are about forty million spermatozoa each time a man…ejaculates. Of those, twenty-five percent will be dead with thirty percent normal in shape and form. This…specimen has upwards of one hundred million with only three percent dead. The amplified motility increases by several factors the possibility that one or more of them will be able to traverse the distance to the ovum and achieve…fertilization."

Teyla leaned forward. "To whom does it belong?" She knew the answer but felt compelled to ask.

The humiliation was a foregone conclusion for John and Rodney, and by extension, her so she just plugged away. "McKay."

Woolsey avoided looking at the two men, shifting slightly in his seat as if it were himself they were talking about. "What about Colonel Sheppard's ATA gene? Why did it stop working?"

"It didn't stop working." Breathing out then in again, Jennifer looked down at her hands as she turned the remote around and around. "It's been removed from his genetic structure."

The room stayed in stunned silence for some time then the monitor changed again. Now displayed were two sets of DNA helixes. "The strand on the left is Sheppard's. See here, here and here?" Several places on the spiral began to blink. "That's where ATA normally resides in someone with the naturally occurring gene. As you can see, those markers are now missing." The image on the right highlighted. "Here and here are where the markers should be when the therapy is successful in artificially creating the gene using the retrovirus." Different areas began flashing. "This is Rodney's DNA. He now possesses the strongest gene on the base." Once more she paused because her next bit of information would be the biggest bombshell of all the bombshells she'd dropped today. "Somehow, that machine removed John's ATA gene and transferred it to Rodney in addition to a small amount of his normal DNA. If I were looking _only_ at their DNA…" Several places on both images flashed. Even to those not familiar with DNA could see that they were eerily similar. "…I would now have to conclude that they are related, however distantly."

Rodney grinned, relaxing at last. "I've always wanted a big brother. Does this mean I'm in gonna be in your will?"

~~O~~

Jennifer turned to give Rodney one of her please-stop-talking looks, but it changed into something entirely different, trepidation.

Rodney normally sat forward in his chair, his feet flat on the floor or crossed at the ankles, sometimes drumming his fingers fretfully on the table or desk, especially when he was getting bad news. Now, however, it was…different.

John was sitting in his customary relaxed attitude, right ankle resting on his left knee, leaning back with an air of casualness that he'd no doubt perfected over the years and she didn't buy for a moment. And beside him, his body arranged in the _exact_ same posture, was Rodney.

She looked from one to the other in a classic double-take that went unnoticed by everyone.

~~O~~

Woolsey calmly took in all the information Jennifer had just imparted and only had one question. "Why?"

"We're not sure. We're still examining the data." Jennifer looked at Radek who shrugged and nodded. "We _think_ the Wraith were working on two different methods of eliminating the Ancients as enemies: sterilization and the transfer of the ATA gene to themselves so that once the Ancients were gone they'd be able to make use of the tech. They obviously didn't take into account that humans would eventually be able create a way to artificially introduce the gene."

"What does this mean for me?" John asked.

"Again, we're not sure." Carson answered the Air Force officer. "But for now, you and Rodney are restricted to the base, no offworld travel."

"Me?" Rodney protested. "_I'm _not the one…"

Jennifer gave Rodney a stern glance. "We don't know what other effects this machine might've had on the two of you that haven't made themselves known yet. Until we figure it all out, you're both staying where we can keep an eye on you."

Woolsey glanced at both men for the first time. "I agree with Dr. Keller."

John didn't say anything, just nodded acceptance. Rodney did so as well though reluctantly.

"Major Lorne, your team will now be the lead offworld team until a cure is found for the Colonel's…condition. Colonel Sheppard will continue as the commander of the military forces."

The military 2IC kept his expression neutral. "Yes, sir."

The meeting broke up a few minutes later, Lorne stopping in front of John, saying everything in a glance then was gone.

Ronon and Teyla hung back to speak to their friend. Teyla touched John on the arm. "Do not worry, John. I'm certain a cure will be found."

"Yeah," Ronon added. "And if they don't no big deal."

"Maybe not for _you_, Chewy, but the gene was the _one thing_ that made me different from all the other soldiers on this base. Without it, I'd still be a Major ferrying General O'Neill back and forth to Antarctica, the SGC and Area 51."

"You are an exceptional leader, John. Many on this base have said so on more than one occasion." She gave him a smile. "They would not replace you just because of this."

"Maybe. Either way, McKay has my gene and I want it back. Now we just have to figure out how to do that." John got a disagreeable glint in his hazel eyes.

"Want a beer?" Ronon asked his friends.

"Thank you, but I must see Torren before he goes to sleep." Teyla gave John one last smile of sympathy before going.

"You and me?"

John tried to look like he was thinking it over. "Thanks, Chewy, but I'm kinda tired. Think I'll just get a shower and go to bed early."

~~O~~

The men parted on the barracks level, Ronon watching his friend walk away knowing there was nothing he could do or say that would make the news he'd received today easier to take. John would handle it in his own way. All the Satedan could do was be there if-_when_ he was needed.

~~O~~

Hours later, and at Carson's insistence, Amanda left the Infirmary to eat and rest a few hours before diving back into their research on how to correct John and Rodney's conditions. She watched from the doorway as Radek and Carson sank back into the data taken from the machine that had done such a terrible thing to her friends.

As she walked the corridors of Atlantis she thought about John. They'd been friends for a long time but had lost touch a few years before they both somehow ended up working for a top secret space agency. It had been a shock to see his name on the crew listing for the expedition and she'd wondered if things would or could go back to the way they were. She needn't have worried. They'd slipped seamlessly back into their easy camaraderie, picking up where they'd left off all those years ago.

Lately, though, she had the feeling that things between them were changing, that they might be on the road to becoming more than just friends. At least that's how _she_ felt. She had no idea what John was thinking most of the time though she went to great pains to convince him otherwise. He used to be a little more demonstrative, but that was a long time ago. He'd closed himself off from others, preferring to keep his emotions under a tight rein.

After debating the pros and cons with herself on numerous occasions, she had decided to keep their relationship platonic. If they took the next step and it didn't work out, they'd still have to work together. Not to mention that his track record with relationships wasn't good, but then neither was hers.

Amanda pushed thoughts of Brody from her mind and when she looked up found that her subconscious had led her to John's quarters. _ He's probably not even here. _With a sigh, she touched the chime.

~~O~~

John had just pulled on his pajama pants and T-shirt when the chime sounded. His spirits lifted at seeing his long-time friend, more than he thought they would considering the news she'd given him today. Standing back, he ushered her in, the door whooshing closed behind her. As she passed him, he inhaled. She smelled of jasmine and vanilla mixed with that unidentifiable aroma that always made him think of her. They'd never crossed the friendship line and it bothered him that he was now considering doing just that. _Where'd __that__ come from? And what makes you think she wants someone who can't give her kids?_

Her eyes were light hazel, big and round with tiny laugh lines at the corners. Instead of aging her, they made her look young and vibrantly alive, happy. The only time he'd ever seen them dull and lifeless was when Carson had died.

When they first met, her hair had been a lighter shade of blonde, almost white, and very short. Now it was honey blonde with lighter streaks and reached to just below her shoulders, curling gently around her face. He flexed his fingers as if he could feel the softness of the curls fluttering over the back of his hand.

"How you doing?"

His head snapped up as if he'd been in a trance, one side of his mouth lifting in a small smile. "Other than not being able to do my job or make any mini-Sheppards, tired."

"Understandable." She handed him another bottle of blue liquid. "You're electrolytes are out of balance. This will help."

John walked past her to set the bottle on the desk. As he turned to say thanks, her hands came up to frame his face and suddenly she was kissing him.

**TBC**


	4. Knitting the Troubled Spirit

**A/N:** Many, many thanks to ladygris for her assistance with this story. It helps to have someone to talk to when the storyline becomes so tangled that you don't know up from down.

Thanks,

~ Sandy ~

**Threads**

**Chapter 4**

**Knitting the Troubled Spirit**

After a moment's hesitation, John's arms gathered Amanda close to his chest and he kissed her back. Reaching behind him, he found the chair he kept for guests, the soft, comfortable one that helped him unwind after a difficult day of sparring with Teyla or Ronon, killing Wraith or having his DNA altered. Without letting go or stopping their kiss, he sat down and pulled her onto his lap. When her backside came into contact with his thighs, a moan worked its way up his throat to collide with the one coming from her.

Pulling his mouth from hers, he kissed his way down her neck and around behind her ear. When he touched that spot with his tongue, she gasped and dug her fingers into his hair and shoulder. His right hand on her back slid up into her hair and a thrill went through him. Those tantalizing strands were as soft as he'd imagined them to be.

As if it had a mind of his own, his left hand dropped to the hem of her light blue top and worked its way under the edge. Just as his fingers touched her stomach, her right hand encircled his wrist stopping him from going any farther. He heeded her unspoken command instead skimming along the outside, around her waist and up along her spine, skipping over the clasp of her bra to join the other tangled in her hair.

Amanda pulled his head up so she could kiss his lips once more only now it felt different, like she was backing off and he did the same. It was a good thing they did because he'd almost reached the point of no return. From the rasping of her breath against his cheek she'd nearly reached that point too.

When she stood up, he did as well missing her touch, the warmth of her body against his. It was all he could do not to reach for her again, to sink back into the heat they'd generated together but sensed it wouldn't be welcomed, at least not yet. He let his hands rest on her waist and touched their foreheads together. "Oh, Mandy."

~~O~~

Jennifer cried out and collapsed onto Rodney's chest. "Oh…my…" The perspiration on her skin made them both sticky where they touched. He gathered her close anyway, kissing her temple, forehead, eye and nose as she lifted her head to look at him. "_Where_ are you getting all this energy?"

"Don't know, but I _like_ it." He trailed the fingers of his right hand up and down her back drawing random patterns on her heated flesh. They stilled when he thought about what she said. "Hey, are you saying…"

"No! It's just that…" she leaned up to kiss him on the chin, "…you usually have to…recharge longer than five minutes in between. Not that I'm complaining, mind you. I'm just saying."

"So…no complaints?"

"Definitely not." Her right hand touched his bicep running across his shoulder and up to cup his cheek. She rubbed her thumb over the corner of his mouth. "Two times a couple nights a week is normal for us and this was…"

"Mmm…four."

She could hear the satisfaction and smile in his voice. It made her smile too. Snuggling deeper into his embrace, she closed her eyes and sighed with contentment. A short time later she gasped and her eyes snapped open again. "Rodney!"

He said "sorry" in a tone that said he wasn't sorry at all then rolled to the side with her still against his chest. "How about we go for number five?"

Jennifer yawned and slid away from him, turning to sit on the side of the bed. "Sorry, honey. I have to get to sleep soon. There's a lot of work to do if we're gonna figure out how to cure you and John."

"What if I don't _want_ to be cured?"

"If we can figure out how to give him back his gene and let you keep it too, we'll do it. Otherwise…" she shrugged. Rodney's arm snaked around her waist as he leaned up to kiss her behind the ear. She dragged her fingers over the back of his hand up to his elbow and back. Encircling his wrist, she lifted his arm so she could stand, groaning as she headed for the bathroom. "I'm gonna walk funny for at least two days and it's _your fault_, McKay." At the bathroom door, she looked over her shoulder to see him resting on his elbow with his head on his hand, a huge grin on his face.

"No regrets."

He heard the water come on and the bathroom door opened again. "Rodney, come wash my back."

"But I thought were out of, you know, extra protection."

"We'll work something out. Now get in here."

~~O~~

Amanda had come to John's quarters to offer comfort if he wanted or needed it, never intending to turn this into anything more than one friend being there for another. But when he'd turned to face her after setting the bottle on the desk, just for one unguarded moment before his mask fell back into place, she'd seen beneath to the fear he refused to show even to his closest friends. She chose to ease that fear in the only way she knew would be accepted, but once her lips touched his she couldn't stop, didn't want to stop, her reserve vanishing in the dim light of John's room.

One of his hands touched her hair, lightly tugging on the strands and making her scalp tingle. The feeling was so intense she couldn't help the sound of pleasure in the back of her throat. His fingers worked their way under the hem of her top to touch her stomach and that scared her just a little. She'd seen the damage that could be done by moving too fast and chose to slow down now while they still could. After removing his hand, her palms touched his cheeks and she raised his head to give him one last kiss. When she got to her feet he followed and after a short pause let his warm hands rest on her waist. Their foreheads touched Athosian-style and she couldn't help giggling when he said, "Oh, Mandy."

"Thought you didn't like Barry Manilow." She leaned back so she could look into his eyes and saw that they'd darkened with desire. She blinked to hide the same in her own.

"Don't, but then you're nothing like the Mandy in the song either." His hands left her waist and came to rest on her upper arms below the short sleeves of her top, sliding down to take her hands in his. "I'm not sending you away, but I understand if you want to leave."

She let out a relieved sigh. "It's not that I…you see it's…"

"You're thinking of that creep Brody again, aren't you?" At her nod he growled, partly in anger and partly in frustration. "Shoulda beaten the crap out of him when I had the chance."

Now she was smiling. "You did get in _one_ good shot before he ran away. But at least he's out of my life and not just because I live in another galaxy." Her hands fell away from his shoulders as she took a step back, letting her arms ease down to her sides. "We should talk about this…" she waved a hand back and forth between them.

"Let's not and say we did."

Amanda wrinkled her nose. "We'll just take it slow and see where it goes, at least for now." She took his agreement for granted and gave him a last soft kiss before leaving.

~~O~~

John watched Amanda toss a smile over her shoulder just before the door closed on her promise to check on him in the morning. He was looking forward to her visit more than he thought he should even under the circumstances. Unfortunately, his subconscious reared up and made him doubt her _and_ himself. _Does she really want me or was it a pity make-out? Either way, we should stop now before it's too late. Unless it's already too late. No, it's not…or is it? I don't know anymore. Or do I?_

Vowing not to fall for her, he decided not to be here when she made her visit in the morning. If she wanted to examine him, she'd have to find him first and he would _not_ make it easy.

He paced around his room waiting for his body and mind to calm down so he could get to sleep. When that proved futile, he sat on the side of the bed and reached for his guitar. He played a couple of Johnny Cash songs and the wheels in his head slowed down though they didn't stop completely.

With a deep, heartfelt sigh, he pulled out a song he'd learned to play in college when he first met an attractive blonde on the road to becoming a doctor and medical researcher. He stopped in the middle of the song because it really wasn't helping, put the instrument aside and lay down to stare up at the ceiling.

~~O~~

Opening his eyes, Rodney found himself lying on the ground in a thickly wooded forest. It was dark and the sounds of the night came to him. The moonlight filtered through the branches of the trees giving the area an eerie glow. Automatically, his left hand reached up to activate his headset but it was gone. That same hand dropped to his left shoulder for the radio but it too was missing. In fact, he wasn't wearing his black mission uniform. He was in pajamas and was barefoot. "Hello? Is anyone there? How did I get here?"

There was no answer so he climbed carefully to his feet. He recognized this place. It was the planet on which they'd first encountered Ronon and Ford had deliberately jumped into the Wraith culling beam to avoid capture.

"Sheppard? Ronon? Teyla?"

He started moving between the trees carefully placing his bare feet to avoid rocks and branches. When he reached the path, he stopped to get his bearings. Directly in front of him was the small clearing where he'd been suspended upside down as he watched Ford and Ronon fight. It had been the first time he'd seen the Satedan and he almost smiled in remembrance but that expression was gone as quickly as it came when the snapping of a twig echoed in the relative quiet of the forest. Someone was here with him. Someone who didn't want to identify himself.

"Major Lorne?"

Suddenly, a Wraith burst out of the trees and Rodney turned to run in the opposite direction. He ran and ran, dodging trees, bushes and low hanging branches. Up ahead, he could just see the DHD. Increasing his speed, he'd nearly reached the device that would take him home when a second Wraith stepped onto the path in front of him and he stumbled to a halt.

It was not the habit of the Wraith queens to leave their ships except to visit another hive so what was she doing here? But this queen was different. Instead of very long fuchsia, vermillion orange, glowing coral or even wild violet colored hair, hers was barely to her shoulders and blue-black. She was also nearly a head shorter than he.

A malevolent glint appeared in her eyes as she walked slowly toward him, the male Wraith stopping him from running away again. Her hand came up to brush the backs of her fingers down his cheek, along his jaw, turning to let her fingertips brush down his throat. Those same fingers grasped the collar of his T-shirt and jerked downward ripping the material and exposing his chest. Her eyes, which had stayed locked with his watching his fear build until it changed to terror, dropped to the area over his heart.

Suddenly the scene blurred and changed.

Rodney looked down at his right hand, the skin strangely pale. Turning the hand over, he saw the feeding organ in the center of the palm. Flexing his fingers, he brought his eyes up to meet those of his prey. She was small as humans go but he could taste the strength of her life force across the small gulf between them. Her brown eyes looked back boldly, without a hint of fear. With a snarl of victory, he drew back and slammed his feeding hand against her chest.

~~O~~

Teyla shot to a sitting position in bed, sweat pouring down her face and taking in great gulps of air. Kanaan had taken Torren to the mainland so she was alone in her quarters. Bringing up the lights, to chase away the darkness, she climbed out of bed and went into the bathroom. Unbuttoning the front of her pajama top, she examined her chest and was relieved to see that it did not bear the mark of a Wraith feeding hand.

The nightmare had started out with her in her former persona as the Wraith queen about to feed on Rodney. Their roles had somehow become reversed and he'd begun to feed on her when she'd forced herself to awaken. She pondered the meaning of the vision as she showered and dressed for the day.

~~O~~

Sometime later, Rodney carried his tray to the team's usual table for their customary team breakfast meeting. John and Ronon had already finished eating and were talking with Evan. He sat down, took a sip of coffee and picked up his fork. Just as he brought the first bite of pancakes to his mouth, he got the strangest sensation, as if he were being watched. Still jumpy from the nightmare, he turned quickly and saw Teyla approaching, an odd look on her beautiful face, but no one else seemed to be paying him any attention. She set her tray hesitantly next to his and cast a quick glance around the room, her eyebrows drawn together.

"Teyla?" John asked when he saw her hesitate before sitting.

"I'm sensing…if I did not know better…"

"What?" This from Ronon.

"It is the same feeling I get when Wraith are near." She sighed and sat down.

John shrugged and took a long drink of the blue stuff Amanda had told him to drink only this time it was purple. "Except for Todd, they've been suspiciously quiet lately."

"I'm sure it's nothing." Picking up her fork, she began eating.

Next to her, Rodney was doing his best not to react when a sense of panic set in. Adrenaline began coursing through his body initiating his fight or flight instincts. It was all he could do to keep himself from running from the room. His right hand dropped to where his nine mil would normally be but he turned it into a thigh rub.

He didn't like this feeling of impending doom. Trying to ignore it, he took a few more bites of the pancakes but it made him queasy. Pushing it away, he tried to pay attention to the conversation between Evan and John as the Major was brought up to speed in his new _temporary_ position as head of the premier offworld team.

Finally, Rodney couldn't take it any longer. He stood and hurried from the Mess Hall through the patio door. When he reached the rail, he gripped the top edge tightly trying to quell this feeling of panic that had gripped him. Then, just as suddenly as it had appeared, the feeling was gone. He let out a breath he hadn't realized he'd been holding. With a sigh, he went to his lab and went back to work.

~~O~~

Teyla twitched her shoulders as the feeling of dread eased and finally vanished. The rest of the meal passed uneventfully and she was actually looking forward to her first offworld mission with Major Lorne in charge. He'd told her to call him Evan, no doubt in order to put them on slightly friendlier terms so they'd be a little more at ease with each other. And it had worked. By the end of their briefing she had actually laughed at several of his wry jokes.

~~O~~

John watched Rodney jump up and run out the patio door. Nodding in that direction, he asked, "The hell's wrong with McKay?"

Teyla shrugged one shoulder, a shiver shimmying down her back. "I do not know. We have had no need to speak since we returned from M7M-536."

"Huh." John tapped his headset. "Sheppard to Keller."

When he was done filling Jennifer in on Rodney's odd behavior, he spotted Amanda entering the Mess Hall, her eyes scouring the room determinedly. He slid down in his seat and said a hasty good-bye to Jennifer before easing out of his chair so he was below the level of the table. He put a finger to his lips then duck walked to the nearest exit. A quick glance around told him that Amanda was gone and he breathed a sigh of relief. Getting to his feet, he activated the door while congratulating himself on getting away. He'd only taken two steps when a voice stopped him in his tracks.

"John Sheppard."

The Colonel tried to cover his shock at being caught with a nervous grin. "Hey, Doc. I've been looking all over for you."

"Well, you didn't look in the Infirmary because that's where I was. After that, I was at your quarters where _you_ were supposed to be." Amanda stood back and made an after you gesture. John sighed with resignation and accompanied her to the Infirmary level.

~~O~~

Radek came into the science lab, his hair still damp from the shower. He gathered up his equipment and was nearly out the door when Rodney came out of his office.

"And where the hell do you think _you're_ going?"

Pausing at the door, Radek turned to face him, his glasses reflecting the overhead light. "Major Lorne is leading a team back to M7M-536 to examine the device that injured Colonel Sheppard."

"And _me_! Why wasn't I informed?" He tapped his headset. "McKay to Lorne."

"_Lorne. Go ahead._"

"I'm coming with you." Rodney was already out the door and headed for his quarters to change into his mission uniform.

"_Negative, doc. You're restricted from offworld travel, remember?_"

"I know. Don't leave yet." Changing his course, he headed for Woolsey's office.

~~O~~

Evan looked up as Rodney made his way into the Jumper Bay. He waited but the physicist didn't say anything, just kept glancing around as if he thought he was being followed then found a seat in the back. The hatch had started to close when they heard a female voice calling out.

"Wait! Stop!" Jennifer ducked under the half closed hatch, a Glock strapped to her right thigh and carrying a field medical kit. "If you're going, I'm going." The Marine sitting next to Rodney gave her his seat. "Okay, Major. We can go now."

"Flight, this is Lorne. Jumper three is _finally _ready to depart."

"_Flight to Jumper three. The 'gate is dialed. You may depart at your discretion_." Chuck's voice came through his headset as the ship lowered into the Gate Room.

Seconds later they were on M7M-536. On this trip, Evan, in addition to his own team, had brought a squad of men plus Teyla, Ronon, Rodney, Jennifer and Radek. He landed the Jumper to let out the squad that would guard the 'gate, lifting off again to follow the same flight path that SGA-1 had taken on their previous trip. He also debated how to handle the assignments when they arrived at the facility. If that machine did what they thought it could do, well, he didn't want to be anywhere nearby if it came on again and neither did the rest of his men and women. They'd just have to be extra careful.

**TBC**


	5. Pieces of the Whole

**A/N:** Thanks again to ladygris for her assistance with this story.

~ Sandy

**Threads**

**Chapter 5**

**Pieces of the Whole**

Amanda had John lay on one of the empty beds while she did her examination. He kept trying to see what she was entering in his file but she had the monitor turned away. A few minutes later, she pulled back the privacy curtain and called Marie. She made notes on a tablet then passed it to the nurse. "Here's the tests we need done." Marie nodded and turned to inform the phlebotomist but stopped at Amanda's next words. "Oh, and Marie, Colonel Sheppard's been a bad boy. Use the _big_ needles."

Marie grinned. "Yes, doctor."

~~O~~

"How're you feeling today, Colonel?" Carson inquired as he approached John's bed.

John had been alone in the Infirmary ward for almost forty-five minutes and was bored beyond tears. He'd thought about sneaking out but decided to just hang out until he was released. "About how you'd expect, doc." He took a long drink from the bottle of blue stuff that Amanda kept pushing on him. "What's on your mind?"

"I just need to give you this injection and you can be on your way."

Carson wrapped a tourniquet around John's bicep and tightened it. "What's it for?"

"Just something to help you feel better." He cleansed the area and completed the injection.

"So, it's a shot of Jack with a beer back."

"Very amusing. Off with you now and call if you have any unusual symptoms."

The military man jumped off the bed and rolled down his sleeve. "I grow a third eye in the middle of my forehead or my skin turns a funky color, you'll be the first one I call."

~~O~~

When he was finally released from the Infirmary, John headed for his office. Over an hour later he'd completed as much "paperwork" as he could handle at one sitting completely ignoring the flashing icon on the screen. "Sheppard to Lorne." He paused but received no answer. "Major Lorne, come in." He tapped the headset again. "Sheppard to Tower."

"_Tower. Go ahead_." Chuck's voice came through sounding like he was at the far edge of transmission range making John have to strain to hear him.

"Locate Major Lorne and send him to my office. What? Speak up, Sergeant." The voice of the Gate Tech faded away. Yanking the headset from his ear, John jumped into the nearest transporter and got out at Operations.

~~O~~

Sitting at her desk, Amanda was flipping through John's and Rodney's recent medical histories again to make certain she hadn't missed anything when Marie came in. She looked up and though the nurse tried to school her features, the medical doctor could tell she did not have good news.

"Okay. Give it to me straight."

Marie handed her a tablet with the results of John's latest rounds of test and watched for her reaction. It was common knowledge that she and the Colonel were close long-time friends. What wasn't as easily seen was the fact that Amanda felt more for John than she let on to anyone, including herself.

She felt sad for both of them. John's health was failing and they had no idea how to stop it. Her friend didn't say anything more so Marie slipped out of the room.

~~O~~

"Colonel? Colonel Sheppard?" Chuck tapped at his workstation. "Sir?"

"What going on?" The tech seated at the console behind him asked.

"No idea. He acted like he couldn't hear me then nothing. I…"

John took that last steps to the Operations in one bound, grasping the edge of the console to keep from falling backwards when he overbalanced. "Sorry, Chuck. Must be a dead battery." He tossed the headset to another tech. "What did you say about Lorne?"

"Uh, he's not on the base, sir. He's…"

"Speak up, Sarge. _Why_ are you whispering?"

Chuck exchanged a glance of confusion with his co-workers but was stopped from responding when Woolsey came out of his office, his eyes on his tablet. He stopped at the top of the staircase going down to the next level. "Chuck, call Colonel Sheppard and inform him that Major Lorne has taken a team back to M7M-536."

"Thanks for the intell, Woolsey."

"Colonel." The expedition commander looked John up and down. "You're looking well."

"Looks can be deceiving. Why wasn't I told about the mission?"

"If you bothered to check your email now and then, you wouldn't be asking. They were given the green light while you were in the Infirmary."

"Oh. Sorry."

"Well, good to see you up and around. Chuck, I'll be in my quarters." Woolsey nodded to everyone and continued on his way. It wasn't that he didn't care about John. For a diplomat, a man who'd made his living using words to create emotion or to diffuse it, he had precious little to say to someone he hadn't gotten to know as well as he should have in his time in Pegasus.

When Woolsey was gone, John faced Chuck again. "Where's McKay, by the way?" The Gate Tech paused long enough for him to figure it out. "If _he_ went, I suppose Keller had to go, too."

"Ronon, Teyla and Dr. Zelenka, sir. They're due to check in at 1600 if you'd…"

"_Colonel Sheppard, please come to the Infirmary. Colonel Sheppard._"

Shrugging, John took the fresh headset Chuck handed him and was gone.

~~O~~

Evan clicked the radio in a pre-arranged signal that meant "suckers on the ground" and Gunnery Sergeant Brackman responded with a double click.

At that moment Teyla realized that she'd been sensing Wraith for some time though it was different from what she felt when in their presence. Some of what she was feeling came from _inside_ the ship. Closing her eyes and breathing deeply, she tried to clear her mind, to bring into focus the moment when she began to have this odd sensation. It started just before Rodney had appeared to join them on this mission. She opened her eyes and watched the physicist as he returned to his seat.

Now was not the time to bring up her misgivings. If she concentrated, she could separate what she sensed coming from Rodney from the Wraith awaiting them on the ground. She had many years of experience at meditation to help her but Rodney was not as lucky. If he was experiencing anything like what she was feeling, he had to be on the edge of panic right now. She would stay as close to him as she could and not have it interfere with her own Wraith sense in case he needed her assistance.

~~O~~

Carson looked up from where he was conducting a test whose purpose completely escaped the military man's comprehension. "Thank you for coming so quickly, John. Please have a seat."

"You know, doc, that particular look doesn't instill confidence in your patients." John turned a chair around and straddled it, folding his arms on the back.

"Sorry." The Scot drew a chair up in front of John and touched the remote. "I know you won't understand what you're seeing, but these are the results of your tests. Most of them anyway." More than one test was highlighted along with the results. "I know it was unethical to perform an experiment on ye without your consent but I didn't want to get yer hopes up."

John latched onto the one word that alarmed him more than the others. "Experiment?" Though he appeared relaxed, Carson could see the muscles in his upper back and shoulders tense.

"And please don't blame Amanda or Jennifer. They had no idea I'd be takin' liberties."

"Doc!"

Carson laced his fingers together and rested them in his lap. "That injection I gave ya was the gene therapy." He picked up the LSD at his elbow and handed it to John. It went dark when the Colonel touched it. Carson touched the remote again and slowly twirling DNA strand appeared on the monitor. "I'd hoped that, having once had the gene, the therapy would reinstate it. When it's successful, ATA will be found adhering to and integrating with your DNA at these points." With a silent sigh, he turned back to John seeing the disappointment in his eyes for just a second then it was gone, replaced by a blank mask. "As you can see…"

John levered himself off the chair and turned away. "Thanks for tryin', doc."

"John, I'm…" Carson didn't get a chance to finish because he was gone.

~~O~~

With the Jumper cloaked, Evan did a flyover and located several Darts hidden in the forest. He momentarily wondered why they'd come in Darts instead of on foot, why they hadn't immediately dialed out so no one could dial in or escape, why the 'gate hadn't been guarded and where the hell the Hiveship was.

Rodney was standing behind him again poking at his computer and watching the HUD. A light was flashing on the icon that was the Wraith lab. "Yes, Major. A subspace beacon is, at this very moment, calling out to every Wraith ship in the vicinity. It wasn't there when we returned to Atlantis so it's only reasonable to assume it became active after the fact." He looked down when Jennifer came forward and took his hand. "A few have already arrived early for the party. By the way, we need to get inside before they do."

"Got it. Have a seat. We're landing."

~~O~~

The door to the main workout room slid open and John stalked in. He tossed a towel and sport drink on the bench as he moved to the center of the room. After a quick warm-up, he went to the punching bag. The longer he punched it the angrier he became. Finally, he slammed it one last time really hard then went to the locker for a set of Bantos rods.

He was ten minutes into the forty-minute routine Teyla had shown him when he became lightheaded causing him to stagger against the wall. Closing his eyes, he willed the room to stop spinning and eventually it did. Taking a few gulps of air, he pushed off and moved back onto the mat walking around until the muscles of his thighs stopped quivering and the strength returned to his extremities. He rolled his shoulders and raised his arms into the ready position again starting at the beginning.

This time he made it most of the way through, coming up on a double spin, duck and roll. He got to his feet and the room swirled making his stomach heave. Staggering the edge of the mat, he collapsed onto his hands and knees, the contents of his stomach splashing on the hard deck. He hadn't eaten much for breakfast, nothing at all for lunch and only had water and the electrolyte-enriched beverages to drink so the amount wasn't great. It was also a disgusting pinkish-purple color.

Using the tail of his shirt he wiped his mouth and leaned his back against the wall squeezing his eyes shut. When everything stopped spinning he got to his feet, grabbed his towel and cleaned up the mess. Retrieving his drink bottle, he carried the towel down the hall and tossed it into the incinerator.

Back in his room, his legs didn't feel as if they would hold him long enough to shower so he ran a bath. Tossing his clothes in a corner, he sank into the hot water, rested his head on the back edge of the tub and closed his eyes.

~~O~~

Ronon, Teyla, Billig, Reed, Coughlin and Lorne left Rodney, Jennifer and Radek in the cloaked Jumper and headed out to intercept the Wraith nearing the lab. They spread out and crept silently through the forest. A sharp inhale from Teyla at Lorne's right caught his attention. She nodded once and he turned back to watching the forest, his left hand dropping to the radio. Click-click-click.

~~O~~

AJ ended up with Ronon. The Satedan wasn't much for talking and they were on radio silence so all was quiet. A sound to AJ's left had them both on alert. Ronon's hand pressed down on his shoulder at the same time he put a finger it his lips for quiet. Nodding, AJ gripped his P-90 tighter as two Wraith passed within two meters of their hiding place.

He watched them scan the area as they passed in the direction of the lab. When they were out of range, AJ clicked his radio.

~~O~~

Nick and Paul crouched behind a fallen tree as three Wraith paused in front of their hiding place. They heard one of them growl as if he could sense the humans nearby. Exhaling slowly in relief, Paul clicked the radio to let Evan know the number of Wraith they'd seen. Click-click-click.

~~O~~

Rodney counted the radio clicks. There were eight on the ground, all headed for the lab. They had to stop them before they did something stupid like blow it up before he got a chance to examine the device. He pretended to be unaffected by the fact that he now had John's ATA but it had him concerned, and not just for himself or for John. Atlantis needed John as much as it needed _him_. Yes, he knew it was arrogant for him assume that the city would fall apart without him but that didn't stop his thoughts.

He paced, rubbing his hands together while Radek and Jennifer watched. They'd tried to calm him but it only irritated him so they stopped. When he reached the hatch on his next lap he stopped cocking his head to the side.

"What is it, Rodney?" Jennifer asked.

For an answer, Rodney took his nine mil from its holster, checked the magazine was full then replaced it. The P-90 he'd set aside earlier he picked up and attached to the neck strap. "Both of you _stay here_. Do _not_ open the hatch again until I tell you to and do _not_ leave. And don't think for a moment that I'm kidding."

"But Rodney…" Radek didn't like the tone of Rodney's voice. Apparently neither did Jennifer because she touched him on the arm giving him an almost imperceptible shake of her head.

After taking a quick scan, Rodney hit the hatch release and stepped outside. "Stay!"

As the hatch closed, they watched him raise his weapon and move off into the forest.

~~O~~

Even after his bath, John was fatigued, lightheaded and all of his muscles ached. Ignoring his condition, he paced from the Operations console to the rail over to the bridge and back to Operations over and over. His people had been gone for several hours with no contact. _I should be leading this op not cooling my heels away from the action._

Finally, Chuck couldn't take it anymore. "Colonel, why don't you go get something to eat or take a nap or, um… I'll contact you when I hear something from Major Lorne and his team. They're due to check in soon."

A sheepish smile crossed John's face as a hand rubbed the back of his neck. "What you're really saying is 'go away, you're bothering me', right?"

"Well, I wouldn't have put it in those words _exactly_, sir, but…" Chuck shrugged, one side of his mouth curling upwards.

"Point taken, Sarge. I'll be in the Mess Hall…or the bar." He turned a little too quickly and the room spun. Dark spots formed in front of his eyes and the next thing he knew he was on the floor with his feet on the seat of Chuck's chair with the Gate Tech crouched next to him.

"Colonel? Are you alright, sir?"

He lifted his head, found the room was still spinning though not as fast and squeezed his eyes shut. "Wha' happ'n?"

Before the Gate Tech could answer, Amanda and a medic rolled a gurney onto the scene. "Sergeant Campbell called us, said you fainted."

"I didn't _faint_," John responded hotly. "I…passed out."

"Of course you did, Colonel." Amanda completed a hands-on assessment then took one of John's arms while Chuck held onto to the other as they helped him to stand. "Come on. I'm admitting you to the Infirmary."

"Like hell you are!" He yanked his arms from their hands and almost fell again. "On the other hand, a ride might be nice." The medic came forward and together he and Chuck helped John onto the gurney. Amanda buckled him down then attached the EKG and EEG monitors. The medic raised the head up before pushing the gurney toward the bulk transporter. John folded his arms under his head trying to appear casual and in control though he felt anything but. "Let's cruise past the Santa Monica beach. I wanna watch the girls play volleyball."

"You're in no condition to be ogling women, Colonel." Amanda's tone held amusement she didn't feel. "Besides, most of those girls are barely legal. I know. I used to be one of them."

John's arms came down and crossed over his chest, a false frown on his handsome face. "You, Dr. Cole, are taking all the fun out of life. Mine at least." That was a lie. When she mentioned that she'd been a teenaged beach bunny that was all he could think about. His mind substituted her white lab coat and uniform for a red bikini and volleyball, her fair skin tanned by the California sun.

"You'll get over it. Probably by the time we get to the Infirmary."

~~O~~

Rodney still hadn't figured out what was causing that weird creepy feeling. All he knew was that the urge to fight or flee was back. Evan and the others needed his help. He couldn't explain _how_ he knew it, he just did. Crab walking from bush to bush, the being watched sensation climbed to gargantuan heights.

Up ahead he could see two figures crouched in a stand of bushes and headed for them. When he got close Nick and Paul spun around, aiming their weapons. They slumped in relief when they saw who it was.

"What're you doing out here, doc?" Paul whispered.

"Thought you'd need some help."

"But the Major said to stay put. You're gonna get yourself killed."

With an indifferent shrug, Rodney reached for his radio and clicked it five times. "That brings the count up to thirteen. Bad luck."

"Thirteen?" Nick was confused. They hadn't seen that many Darts.

"Yeah. And headed this way. I…" The physicist stopped talking as he peeked over the top of their haven, his eyes scanning the greenery in front of him.

Nick joined him but didn't see anything. He looked down to exchange this-guy-is-nuts glance with his teammate.

Paul's nerves were on edge as well but he refused to put himself in greater danger by giving the Wraith an easier target.

Suddenly, Rodney turned and fired, cutting down two Wraith running in their direction from the other side of the clearing. That set off the others and the air filled with the sound of gunfire interspersed with the sharp whine of Ronon's energy pistol and the Wraith stunners.

~~O~~

John didn't get over his fit of pique for quite a while. He was put through test after test though thankfully he didn't have to do a particular one again. To tell the truth, he didn't feel as if he could produce a specimen. He didn't want them to know that or they'd keep him even longer.

Marie came in and inserted an IV. He complained the entire time though she ignored everything he said and kept working which she knew annoyed him.

Amanda came in just as she finished. "Okay, Colonel. Time to take your temperature." She reached into the cabinet under the monitor. John turned his head to the side waiting for her to stick that thing in his ear, but she didn't. When he looked at her again she was shaking a slender piece of glass. "We're doing it the baby way this time. Roll over onto your stomach and drop 'em."

He clutched at the covers pulling them up to his chest, his eyes wide. "Excuse me?"

Hiding a grin, Amanda tried to yank the covers down and the two of them engaged in a tug of war that ended when she started laughing which got him going too. Eventually they calmed down and she set the thermometer aside. "Glad you're feeling better." She traded her grin for a serious mien. "John, you passed out due to a combination of things. Your blood pressure was low, you're dehydrated, and your blood sugar dropped suddenly. Add that to your electrolyte imbalance and…"

"…I'm kissing carpet." He blinked a few times and sighed. "So give me a bottle of that stuff and I'll go get something to eat."

"Mmm. Not so much. We're keeping you a little longer, just a few hours. And for now, you'll be getting some of your nourishment from this little fella right here." She patted the IV bag hanging above his head.

He decided to give in gracefully for once giving her his most charming smile. "Is there a chance I might get time off for good behavior?"

"Highly unlikely." Amanda's lips pursed as she tried to keep from grinning.

"I could argue, but what would be the point? You'd still pull rank." She patted his arm and turned to go but he took hold of her hand keeping her in place. "Uh, Mandy…" his eyes flicked over her shoulder to make sure they were alone and lowered his voice, "…what time does your shift end?"

"1800. Why?"

"Um, wanna go get a beer? With me, I mean."

She poked him in the chest with her free hand. "_Beer_ is not on your diet at the moment."

John shrugged. "So _you_ have a beer and I'll drink the blue stuff. What d'you say? I happen to know you shoot a mean game of pool."

"You got it. One condition."

"Name it."

Leaning close enough that he could see the light sprinkling of freckles on her nose, proof of her former days as a sun worshiper, she lowered her voice to a provocative whisper. "Instead of pool, dance with me."

~~O~~

_What are you doing?_ Amanda berated herself as she left John alone with the meal she'd finally ordered for him. _He's getting worse, you can't stop it and you're __flirting__ with him? Not to mention you haven't given him a full report on his condition yet. Carson would have done it but no, it had to be __you__, his pal from college. _

_And you haven't told him how you feel, how you've felt since shortly after renewing your friendship. _

_But what if he doesn't share those feelings? Are you really willing to put yourself out there and risk having it thrown back in your face?_

By the time she'd reached her office she hadn't come to any conclusions or solutions for whether or not to open her heart though she did have an idea on how to help John. It was a longshot but if she didn't at least try… With a renewed sense of purpose, she called up the files she needed and got to work.

**TBC**


	6. Weaving a Tangled Web

**A/N:** As always, thanks go out to ladygris and dwparsnip for their assistance and friendship. Shadows-of-Realm might have helped but he's been busy lately with RL pursuits.

~ Sandy

**Threads**

**Chapter 6**

**Weaving a Tangled Web**

When the firefight ended, the Atlanteans met outside the Jumper. Rodney, Radek and Jennifer gathered their equipment together and headed for the lab once again.

Over his shoulder, Rodney spoke to Evan, his tone brusque. "Once we get everything we need from the lab, we should destroy it."

"Yeah. Can't have the Wraith picking up where they left off." Evan sent his men to set C4 charges around the outside while he placed them strategically in the interior.

~~O~~

"The charges are set, doc." Evan hurried to get in front of Rodney striding purposely for the Jumper's open hatch. "Just give the word."

"Don't be so quick on the trigger, Major."

"But you said…"

"I _know_ what I _said_. _Now_ I'm saying don't destroy it. Not yet." The physicist ignored all further conversation from Evan, took the pilot's seat and began the start-up sequence.

Evan started forward indignantly but Jennifer stopped him with a hand on his arm. "Let it go, Evan. He's been acting not himself for a while now. He needs something besides this to focus on."

"Okay. Just tell me _why _we can't blow up the lab."

Despite the seriousness of the situation, Jennifer snorted with mild amusement. "You sound like a kid who's been told he can't play with his favorite toy."

"Doc!"

"Sorry."

Radek spoke up from his seat in the back next to Reed. "We will need to do further research however we believe that now that we understand better how the device works, we will be able to reverse it and restore the Colonel's DNA. Unfortunately, that would mean taking the gene from Rodney. He would then go back to having the artificial gene. As you can see, he is not happy with that idea."

Evan nodded and sighed. Moving up to the co-pilot's seat, he unhooked his P-90 and set it aside. "Ready to go, doc? We'll leave a squad to guard the lab in case the Wraith come back."

Rodney didn't say anything, just nodded and that bothered Evan more than anything, even the physicist starting the firefight with the Wraith. They got them all as well as destroying the Darts just in case. But it was still strange.

~~O~~

Amanda, her head resting on her folded arms tears wetting the skin and tiny hairs, didn't hear her office door open then silently close again. She also didn't sense someone in the room with her until a hand touched her on the shoulder. Lifting her head, she was surprised to see the expedition's only xenobiologist, Chris Rose, looking at her with sad eyes. He didn't say a word, just took her in his arms and let her cry on his shoulder.

"I was hoping the therapy we used to cure Carson would be able help John, keep his physical condition from deteriorating but all the computer models failed. Not only won't it help, using the therapy might exacerbate his condition."

"I'm sorry." Chris would have said more but was interrupted when her headset chirped.

"_Sheppard to Cole_."

She pushed away from Chris, brushed the moisture from her face and took a deep breath to steady her voice. "Cole. Go ahead."

"_It's 1817_."

"You didn't call just to tell me the time, John."

"_No. I called to remind you __we__ had a date…at 1800_."

"Oh, sorry. Um…" she glanced at the clock, "…five minutes on the patio?"

"_I'll be there._"

Turning a sheepish expression on Chris, she took off her lab coat and hung it over the back of her chair. "Thanks."

He waved away her gratitude and headed for the door. "No problem. I do have parting words for you though."

"Oh?"

"Death leaves a heartache no one can heal, love leaves a memory no one can steal. I read that on a headstone in Ireland."

Amanda pursed her lips. "Yeah. So?"

"So…go make some memories with him. Best case scenario, you and he could fall in love, get married and adopt a bunch of rugrats. But if the worst case scenario plays out, you'll have more than just being his doctor and friend to remember him by." Chris gave her a jaunty salute before leaving her alone again.

When he was gone, she realized he was right. She smoothed her hands over her hair and checked her look in the mirror. Her eyes were still red rimmed from crying but didn't think John would notice, especially in the dim lighting of the bar. Reaching into her desk drawer, she pulled out a green blouse that made the gold flecks in her eyes glow and accentuated her curves. The neckline was low without showing too much cleavage. A touch of lip gloss and she was ready to go.

~~O~~

Rodney and Jennifer parted as she went back to her research. His plans were to get with Radek and go over the information they'd gotten from the Wraith facility this last time. Halfway there, he changed his mind. Going to his quarters he got into workout clothes and headed for the gym.

When he arrived the room was empty, the smell of stale sweat a constant reminder of the hundreds of people who used it on a weekly basis. For a moment he thought he could smell Jennifer's distinctive aroma. Shaking his head, he dismissed it as his imagination. He stared at the treadmills and bikes but they didn't appeal to him. Not that they appealed to him at any time, but even less so today.

After a momentary thought of going for a run, he went to the lockers, opening and closing them until he found what he wanted, a pair of Bantos Rods. Running his fingers over the sculpted carvings, he moved to the center of the room. Normally he wouldn't think of exercising unless the floor was heavily padded but not today. He kicked off his shoes and took one rod in each hand, swinging them experimentally as he tried to remember what little he'd been taught about sparring.

He hadn't been at it long before he heard the door open behind him. He knew it was Teyla before she'd even come into the room, his mind telling him something was wrong with that picture. She was dressed in slacks and a sleeveless top made of moisture-wicking fabric she'd gotten from Earth.

She carried a bottle of water and a towel, two things he'd forgotten to bring with him. It wasn't like him at all, but he didn't care and the fact that he didn't care sort of freaked him out…for all of three seconds.

~~O~~

John came to his feet when Amanda hurried to his side.

"Sorry. I got busy and…"

"No problem." He gestured and they fell into step together. "I know I promised you a dance but…"

"But?"

Rubbing the back of his neck, a nervous gesture, he asked, "What if we, um…went to my quarters and watched a video instead? I promise to behave."

"Sure. There's just one thing." Her hand on his arm forced him to stop and face her. With a wicked grin, she glanced around then leaned up to give him a brief kiss and a wink. "What if I don't _want_ you to behave?"

~~O~~

"Rodney." Teyla was not surprised at seeing him here. She'd sensed him long before the door had opened.

"Didn't mean to break in on your time." Rodney gestured with the rods, realized what he was doing and laid them on the bench next to her towel and water bottle. "I'll just…"

"That is not necessary. Would you like to spar?" One side of her mouth lifted in a smile. "I promise to go easy on you."

"Uh…sure." After retrieving the rods, he moved out to the center of the mat, warming up by swinging the rods around in circles as he'd seen her, Ronon and John doing then copied her ready stance. Feet shoulder width apart, they brought their left hands out to touch their rods together, paused and…

Rodney swung his right hand across to knock Teyla's left hand away but she was too fast. She swung both hands together and he was just able to get his hands up to block. Pulling his arms apart and swinging in circles, he managed to block and parry each strike, almost as if he knew where her next attack would come from.

Up, down, up, down, left, right, out, around. Over and over.

They paused when Rodney brought both rods up crossed to halt a downward strike. She had yet to get under his defenses and spoke her surprise aloud. "You've been practicing." Barely breathing hard, Teyla gave him another smile.

He shrugged. "Oh, well, you know me."

"I _do_ and you have never shown this level of ability before."

Not knowing what else to do, Rodney shrugged again and while she seemed to be distracted, began swinging hard and fast driving her back.

She rallied and turned the tables on him, stalking him around the room. The rod in her right hand whooshed through the air as she attempted to use one of the tricks that had frequently been John's downfall. Just before she would have whacked him on the backside, he spun around, his right hand coming down to block.

Teyla brought both hands together, spinning to the right as he spun in the other direction, blocking each other's attack. There was a sheen of perspiration on their exposed skin and they were both breathing hard when she finally got the upper hand.

Rodney lost his balance and fell to the mat on his hands and knees. He stayed in that position as she circled around him waiting for him to continue the fight. With a groan, he pushed back until he was sitting on his heels, panting hard. "Time out."

Teyla relaxed, letting her guard down for the first time since she'd sensed his presence in this room. Suddenly, he was on his feet quicker than she would have thought possible. Her arms came up from where they'd dropped to her sides but it was too late.

All evidence of fatigue vanished as he swung his right arm up and around to impact with her rods. He dropped to one knee, the other leg sweeping around and knocking her feet out from under her. She landed on her back and he was on top of her in an instant, his rods across her throat. They were too tight, restricting her breathing.

He grinned in triumph then seemed to realize what he was doing and the pressure on her windpipe eased. Climbing to his feet, he helped her up and following her to the bench under the window. "Sorry."

"Do not be. I was not expecting such a tactic from you. I am impressed." Teyla opened her bottle of water and he watched her take a drink.

Instead of capping the bottle, Teyla offered it to him and he took it gratefully. "Thanks."

She waited for him to speak again but he didn't. "I know this situation is difficult for John to accept though he pretends that it does not bother him."

"Yeah. So?" Rodney used the tail of his T-shirt to wipe the sweat from his face.

"I am wondering how _you_ are feeling. You were not harmed in the way that John was. In fact, this experience seems to have changed you for the better." She hoped he would not see through that falsehood. Rodney was arrogant, condescending and very outspoken, but seldom had she seen the level of ability or aggression he'd shown tonight.

"Uh, sorry to disagree with you, but _I_ am the same now as I've always been."

Though he kept his face neutral, she sensed that it would not be wise to disagree with him. The sensations she'd experienced in the Jumper and while she'd fought the Wraith at his side had changed. They were becoming…darker was the only word that seemed to fit. It reminded her of when John had begun to transform after his encounter with the adolescent female Wraith Ellia.

She would take her suspicions to Jennifer. Something was wrong with Rodney and if all the other odd instances she'd witnessed wouldn't convince the medical doctor then what she was feeling now would be…the clincher.

Calling on her many years of meditation for assistance, she hid her thoughts from him. She smiled and stood. "Perhaps you are right. I'm tired and must be imagining things. Thank you for the workout. We must do it again sometime."

~~O~~

"So? What do you think?" John and Amanda were propped up against the headboard of his bed with a bunch of pillows. He grabbed a handful of popcorn, crunching on a single kernel. His stomach was queasy but didn't want her to know. Instead, he tossed kernels at her pretending it was an accident. She laughed and tossed them back.

"Um, it's…interesting," Amanda hedged.

"Interesting? Is that all you have to say about a 1960's icon?"

She didn't want to insult John's favorite television series but… "I understand why superheroes have to wear the mask. What I don't get, never did get, is the tights and a cape. Doesn't seem practical."

"Wasn't supposed to be _practical_. It just looks cool as you fight or walk down the street with the cape blowing out behind you." He covered a yawn.

Poking him with her elbow, she swallowed the last sip of beer and set the bottle on the bedside table. "Tired?"

Her concern made him a little uncomfortable. "I'm _fine_. The next episode is the first with Eartha Kitt as Catwoman. She was the _best_ of all the Catwomen. The rest in order are Halle Berry, Michelle Pfeiffer, Julie Newmar and Lee Meriwether."

"Bring it on."

John hit the remote to start "Catwoman's Dressed to Kill", scooting close enough to press his right side against her left. When she didn't pull away, he let his head rest against hers. A few minutes later he was snoring softly.

Amanda set the popcorn bowl aside and carefully maneuvered him around until he laid flat with his head on a pillow. He wiggled around getting comfortable but didn't awaken, the remote held loosely in his right hand. She retrieved the remote and clicked over to watch "When Harry Met Sally" but fell asleep before the fake orgasm scene. Rolling onto her side, she snuggled closer when he wrapped his arm around her waist and pressed his face into her neck.

~~O~~

Jennifer listened to Teyla's story and when she was gone, called up Rodney's most recent tests. Examining his DNA again, she found a small anomaly. If she hadn't been looking for it, she'd never have seen it.

"Keller to McKay."

"_McKay_."

"Where are you? We need to talk."

"_On the way to my quarters. Want to meet me there?_"

"Five minutes. Don't leave."

True to her word, Jennifer arrived at Rodney's quarters just at the five minute mark. Before she could announce herself, the door opened. Rodney pulled her inside and into his arms. His lips found hers and she responded to him as always, with a sigh, surrendering to the feelings that being loved by him created within her.

His hands skimmed up and down her back pulling her as close as possible, letting her feel how much he wanted her, would always want her. Every time they touched she felt a small thrill shimmy along her nerves, streaking to every part of her. But through the miasma she remembered that she'd come here for a much different reason. Taking her hands from his hair, she pressed her palms to his chest and moved him back until their lips separated.

"Rodney, _stop_. We have to talk."

"No, we have to make love." He lowered his head to capture her lips again but she turned aside.

They began tussling, and, at first, Jennifer thought he was just playing until he refused to let go of her no matter hard she struggled. In that moment, she knew that there was much more going on than just fun and games. _Her_ Rodney was sweet and gentle when they made love. No meant _no,_ and he respected that. Aggression and violence had no place in their intimate relationship, but what he was doing now bordered on assault. She had to stop him before he did something he'd regret for the rest of his life. Before she put a plan into action, she tried one more time to break through to the man who would do anything for a friend.

"We can't do this now. John needs our help or he'll _die_."

Rodney stopped moving at the mention of his friend and Jennifer was certain she'd gotten through to him. Then she looked into his face. She'd never seen such an expression his face before. He looked maddened yet aroused at the same time. His hands came to rest on her upper arms, his fingers squeezing until it hurt.

"I don't give a damn about _John_. You're _my_ woman, not _his_. Stay away from him!"

Rodney threw her down on the bed and came down on top of her, wrapping his much larger hands around her wrists and confining her arms above her head. His legs trapped hers so she couldn't move. In this position, she could do nothing but struggle weakly against his superior strength and for the first time, she was afraid of him.

**TBC**


	7. The Fall and Rise of the Human Spirit

**A/N:** _Muchas gracias_ to ladygris who patiently acted as a sounding board and brainstorming buddy while I was too sick to think for myself.

~ Sandy

**Threads**

**Chapter 7**

**The Fall and Rise of the Human Spirit**

"Ow! Rodney, please _stop_! You're hurting me! Mmm…" His mouth came down on hers so hard it was almost brutal. Then just as suddenly, he stopped. Jennifer had closed her eyes so she wouldn't have to see the man she loved behaving like a wild animal. He stopped moving and she chanced a peek at him, seeing such a look of horror and disgust she almost cried. There was a gasp and Rodney pushed off of her.

"Oh, my God! Jennifer, I-I'm sorry. I don't know what…" He turned away from her, away from the loathing she no doubt felt for him now, but couldn't turn away from revulsion that he felt for himself.

She sat up and slid off the bed to stand behind him. Tentatively, she laid her hand on his shoulder and he jerked away as if her touch had burned him. "It's _okay_, honey."

"No, it is _not_!"

The intensity with which he said those four words caused a single tear to well up and slide down her cheek. She swiped it away with the back of her hand before he could see it. If he saw her cry and knew he was the cause, it would tear him up inside. He'd pull away, afraid that it would happen again and he wouldn't be able to stop it next time. She'd lose him.

"Go _now_…" his voice was a harsh whisper, "…before I hurt you again."

"No! I love you and we'll get through this _together_."

He swung around, both hands coming up clenched in fists as if he meant to hit her, his face twisted into a snarl. She couldn't help flinching and he saw it, exerting all his will to uncurl his fingers, letting his hands drop to his sides. With a growl born of great aggravation, he suddenly took her hand, dragging her out of his quarters and down the hall.

"Rodney, slow down! _Where_ are we _going_?"

But he didn't slow down, just kept tugging her behind him forcing her to run to keep up. "The Infirmary. I am definitely _not_ the Rodney McKay you know and, hopefully, still love. You need to do tests, lots of them, whatever you want."

"I agree you aren't the Rodney McKay I love, but it'll take more than an aberrant restructuring of your DNA to make me stop."

"Good. I'm, you know, really sorry about…m-maybe you should put a guard on me. No telling what I might do next."

They stepped into the transporter, her hand coming up to tap the screen. "If you're still able to distinguish between right and wrong, guards won't be necessary." They reached the Infirmary level only now _she_ was dragging _him_. "Pick a bed and get in it. Someone will be around to take blood shortly. I came to your quarters to tell you I'd seen an irregularity in your last DNA scan. If what I think has happened has happened, we need to figure this out and soon or John won't be the only one in trouble."

~~O~~

Morning dawned as most mornings did in Atlantis, clear and bright. A brilliant ray of sunshine shown through the stained glass of the window, moved slowly across the floor to touch the foot of the bed. When it reached Amanda's sock covered foot sticking out from under the covers, the warmth brought her awake. She yawned, rubbed her eyes and looked around wondering where she was. Her brain completed its morning restart, reminding her that she and John had spent the evening watching videos and eating popcorn.

Thinking ahead, she hoped he wouldn't be embarrassed about falling asleep during the show. Carefully lifting his arm so she could slip out of bed, she tiptoed to the bathroom. She attended to business, washed her hands then ran them through her hair to smooth down the sleep tousled strands and untangling a piece of popcorn. Squirting a small amount of toothpaste on her finger, she rubbed it over her teeth, rinsed and returned to the bedroom area.

Sitting on the side of the bed, Amanda gave John a shake. "John? Wake up, sleepyhead. It's morning." There was no response which puzzled her as he'd always been a light sleeper, especially since joining the military. "John? John!" Shaking him harder, she pushed on his shoulder so he rolled over onto his back, his head lolling to the side. Her hand found his wrist automatically counting the beats while the other hand rested on his chest counting the inhalations. Both were slow and unsteady. Using the bedside light, she checked his pupils. No reaction.

Her hand reached for her headset, hooking it over her ear. "Medical to Colonel Sheppard's quarters, stat! Medical to Colonel Sheppard's quarters!"

While she waited for help to arrive, Amanda continued with her assessment. All indications were that he'd fallen into a coma. For the final test she would normally have checked the patient's reaction to pain stimuli, but she had something different in mind for him. If he responded…well, she'd deal with the consequences. If he didn't, she'd deal with that as well.

Rolling him onto his side she dug her fingers into the flesh just below the waistband of his pants. He was extremely ticklish in that spot, but didn't even twitch. She eased him onto his back again just as Carson arrived with several medics. Amanda stood out of the way while John was moved from the bed to the gurney. She gave Carson her evaluation of John's condition while they hooked him up to the EKG and EEG monitors and an oxygen mask was slipped over his face.

Following them from the room, she kept her face a blank mask though her mind was in turmoil. She'd planned on taking the risk, putting her heart on her sleeve. Now there was a very good chance he'd never know how she felt about him nor would she know if he felt the same way.

~~O~~

Ronon joined Teyla at the team's usual table. They didn't speak until Ronon pushed his empty tray away and crossed one leg over the other. "You knew what was happening."

"Excuse me?" Teyla had very little appetite and just picked at her food.

"McKay. In the Jumper."

She took a long drink of orange juice before responding. "Not completely. All I knew was that I could sense something similar to yet not quite like the Wraith and that it was coming from Rodney. After our sparring session in the gym, I took my suspicions to Jennifer and she advised me she would handle it."

"Did she?"

Teyla nodded half-heartedly. "He is confined to the Infirmary and under guard."

Ronon didn't say anything for a while, the sadness he felt for his friends evident in his eyes. Those same eyes found hers when an announcement came over the PA that sent them hurrying from the Mess Hall.

"Medical to Colonel Sheppard's quarters, stat! Medical to Colonel Sheppard's quarters!"

~~O~~

Woolsey and Evan, as John's 2IC, were in Jennifer's office as she gave her report on Rodney's condition.

"…as you can see from his most recent DNA scan…" several areas began flashing, "…in addition to the genetic contribution from John, Rodney also has…Wraith DNA."

"Isn't that what gives Teyla the ability to sense the Wraith?"

Jennifer looked down at her hands turning the remote over and over. "Yes, but this is different. The scan we did when they first returned from M7M-536 didn't reveal the Wraith DNA."

"Then how…"

"In the simplest possible terms, it was hiding. While it hid, it grew until he began to be able to sense the Wraith. A side effect from this ability was that he could sense Teyla as well and she him.

"The DNA continues to replicate itself, increasing Rodney's strength and stamina but also boosting his aggression. If it's allowed to continue, it will kill him because the ATA and the Wraith DNA are incompatible. They're fighting each other with the Wraith DNA slowly gaining the upper hand as it overwrites Rodney's human DNA. There's also a progressive increase in his vital signs across the board. That is most likely the reason this particular experiment was abandoned." She was wearing her jacket and keeping her gestures to a minimum so the bruises on her wrists wouldn't show.

"The longer it's allowed to continue, the worse it will become. At the moment, he's being sedated, but we have to keep upping the dosage. Soon we'll have to find another way or risk him having a heart attack, stroke or general organ failure. His body just isn't equipped to handle the additional strain it's putting on his systems." She looked up at their faces then back down to watch her feet shift. "At his insistence, there's a guard on him, two actually. He's not much of a fighter, not in the way Colonel Sheppard is, but his strength has increased to the point where it may not matter. We…" Jennifer really didn't want to verbalize the next part, but it was her duty as the CMO to keep the expedition and the military commanders apprised of any potentially dangerous situations. "He may have to be put in the brig as much for his own safety as well as that of the rest of the expedition. If we don't find a solution soon after that, the next stop is stasis."

Woolsey shifted in his seat, exchanging a glance with Evan. When the door closed behind the diplomat, Jennifer felt her ability to hold it all together vanish and the tears started to fall.

Slipping easily into his self-appointed role as big brother, Evan came around the desk and took her in his arms feeling her body shudder with the force of her sobbing. He didn't say anything, just held her until she put her hands on his shoulders and pushed away. Searching her desk he found a napkin left over from one of the many times she'd eaten while working. She wiped her face free of the tears, blew her nose and stepped back. "Thanks. I, uh, I'll be okay now. Just had to get it out of my system so Rodney wouldn't see. He feels bad enough as it is."

"No problem. Call if you need a shoulder to cry on again, Jen." Loud voices out on the ward sent them both rushing onto the scene.

~~O~~

Rodney watched Woolsey leave Jennifer's office and come to the side of his bed. The sedative helped calm him enough to allow him to have barely civil conversations with others. At least until the effects began to wear off. When he felt himself becoming irrational again, he would call for the nurse and she, or he, would administer another larger dose. But his ability to control such outbursts diminished with every passing hour, his logical mind being overwritten by almost uncontrollable thoughts and feelings of hostility and animosity.

Barely giving Woolsey a glance, he watched and waited for Evan to come out of Jennifer's office but he didn't.

"Well, doctor, how are you feeling today?"

"_Fine_. Why hasn't Lorne come out yet? What's he _doing_ in there with my…with Jennifer?"

Woolsey looked briefly over his shoulder then back to Rodney. "As second-in-command of the military forces he's no doubt receiving further advice on how to carry on with the current…situation."

"_Situation_? Is _that_ what she's calling me now?" The volume of Rodney's voice increased with each word. "She's supposed to _love_ me. _How_ can she treat me like a common _criminal_?" The alarm on his VS monitor blared shrilly into the customary quiet of the Infirmary as his pulse and blood pressure took a sharp upturn.

Rodney reached over with his left hand to pull out the IV but a nurse arrived and quickly injected what looked to Woolsey like a massive overdose of sedative. Rodney's tirade tapered off and stopped as his arm fell onto his stomach short of the IV, his head falling back onto the pillow. He closed his eyes and when he opened them again, Jennifer and Evan had joined Woolsey at his bedside.

Jennifer's hand took hold of Rodney's. "I'm here, Rodney. Just try to relax. We're doing our best to figure this out."

His voice when he spoke was soft and slightly strained, as if he were struggling to get each word out. "…know…sorry…bother…" his hand gripped hers almost desperately, "…love…you…" When Jennifer's hand cupped his cheek, he turned into the touch.

"I know, honey. I love you, too." She stayed with him until he finally fell asleep and when she turned around, Woolsey and Evan were gone, the privacy curtains pulled into place.

~~O~~

Carson led the way into the Infirmary with one hand on the head of the gurney as he maneuvered it into place beside the empty bed next to Rodney. The privacy curtains were pulled around the bed as they worked on the comatose John. Though he was lean, his muscle mass made him heavy and it took four to move his dead weight. Carson moved to the far side of the bed with one of the medics. "On my count. One, two, three."

The flurry of activity continued when Jennifer joined them. Amanda gave her a quick rundown of what she'd observed when she awoke to find him in this condition. When they were confident that John was stable for the moment, they stepped away while the medics removed his uniform, placed him in a hospital gown and a nurse inserted a catheter. The ruined uniform was thrown into the trash though the patches and belt were still salvageable. These were tossed into the bedside table and promptly forgotten.

~~O~~

When Rodney opened his eyes, Jennifer was no longer at his side though he could hear her, Amanda and Carson behind the curtain pulled between the beds. Stretching to the limits of his reach, he yanked the curtain out of the way to see John's still form being worked on by the medical staff. An IV was inserted in his right hand while Amanda took several small vials of blood from the left, passing them to the nurse who carried them to the lab. She didn't need to tell her to rush the results. They all knew what was at stake. He watched them work for a while then let the curtain drop.

He roused himself from his thoughts a while later when a tray of food was placed in front of him. Lifting the lid, he found a turkey sandwich, an apple and hot coffee. Not his favorite but at least they remembered to feed him. He picked up the sandwich, took a bite and spit it out. "This tastes like _crap_! Can't anyone get a decent meal in this place?" Pushing the table away, the tray clattered to the floor, the apple rolling under a bed and coffee splashing across the floor. He pulled the IV from the back of his hand. Ignoring the blood dripping onto the stark white sheets and the front of his scrubs, he kicked the covers off and swung his legs over the side.

"Dr. McKay! Where are you going?" Marie used her most reasonable and calm tones.

"I'm getting the hell _out_ of here, _that's_ where I'm going. Away from this sorry excuse for a hospital and away from this city to a place where I'm appreciated instead of taken for granted. But first I'm going to the Mess Hall for something to eat that doesn't taste like _crap!_"

He shoved Marie to the side and she fell against John's bed as he stalked toward the exit. The guards stood their ground as the physicist approached them with a look of ferocious intent.

"Dr. McKay, please _stop_." To the man's surprise Rodney just laughed.

"Or _what_? You'll _shoot_ me? I'd like to see you _try_." Rodney kept moving, a contemptuous grin on his face daring them to shoot.

The guard who'd spoken pulled the stunner from its holster on his right thigh and aimed.

"Rodney McKay! Get back in bed!" Jennifer hoped the sound of her voice would get through to him but he didn't even slow down as he kept going.

The guard looked at her and reluctantly she nodded. A red bolt hit Rodney in the chest stopping him in his tracks. His body stiffened and he fell to the floor in a heap just as Jennifer and Evan reached him.

Kneeling next to the unconscious man, Jennifer touched his neck below his jaw. "His pulse is very fast." She bandaged his hand then got to her feet directing the guards to pick him up. "We've given him the highest dosage of sedatives possible without risking organ failure. Confinement is the only way, at least for now."

~~O~~

Amanda pulled a chair up next to John's bed and though she knew he wouldn't allow it if he were conscious, she took hold of his hand, rubbing her thumb over the back. His fingers clenched on hers but she didn't read anything into it. People in comas frequently had reflex movement in their limbs.

Suddenly, she didn't care if anyone knew how she felt about their military commander. She let the rail down and laid her head on the side of his bed, one hand resting on top of his where she'd placed it on his chest.

There was a commotion involving Dr. McKay a few minutes later but she ignored it and not long after was asleep.

~~O~~

Evan watched as Jennifer gave the order for Rodney to be taken to the brig and knew it was killing her to do so. If the length of time it took for his last dose of sedative to wear off was a clue, the stunning he received wouldn't last long either. He followed along as the detail carried Rodney into the enclosure and laid him gently on the floor. Once they were outside the detention area, he paused a moment. He didn't want to do this anymore than Jennifer did. Rodney and he hadn't gotten along most of the time, but they'd found some common ground late one night during a sleepwalking incident. With a deep sigh, he engaged the forcefield.

~~O~~

Trudging wearily up to his front door, John thought how good it was to be home after three months away with no one for company but Ronon. The door closed behind him wrapping him in a cocoon of warmth and homey sights and smells. He could hear the voices of his family laughing and talking in the kitchen, taking a moment to consider how lucky he was to have found the woman who'd become his wife. Keeping her and their children in his memory was all that had gotten him through.

"Hey, anybody home?" He announced his presence as he always did when he returned and as always, he was greeted with a chorus of…

"Daddy!" Running feet followed the exclamation and mere seconds later he crouched to gather his son and daughter in his arms. "Daddy-daddy-daddy!"

And just like that, all his troubles faded away as if they'd never been.

**TBC**


	8. Altering the Future

**A/N:** As always, thanks to my brainstorming buddies, mostly ladygris and dwparsnip, for assistance with this story. SoR has been AWOL recently, but he's had a good reason.

~ Sandy

**Threads**

**Chapter 8**

**Altering the Future**

He was lost, wandering through unfamiliar dark corridors often coming to a dead end and having to backtrack to the main corridor. Sometimes he heard footsteps and would hide until they passed. In the distance he could hear indistinct voices pulling at him to join them, whispers in the dark, calling his name. Not his real name, but the name that would be his once he'd joined them, though he had no idea who _they_ were.

Pain in his right hand made him inhale sharply with the force of it. Lifting that hand he examined it in the faint light that seemed to come from everywhere and nowhere at once. In the center of his palm was an opening that looked like a mouth. He slumped against the wall, his long white hair falling forward to brush the sides of his face. Weakness overcame his body, reminding him he hadn't fed in quite some time.

Pushing himself upright, he staggered down the hall using his left hand as a guide until he came to an open area. Figures dressed in dark clothing moved from one task to another, completely ignoring him. Before him was a console that glowed with an eerie light. He grasped the edge lifting his head to see a reflection in the surface of the monitor.

A gasp was torn from him when he saw yellow eyes staring out of a face covered in pale skin with ridges beginning above his nose and continuing at an upward angle where human eyebrows would be. The fingers of his right hand reached out to touch the screen but jerked back when a voice spoke to him.

"You! The Queen demands your presence in her chamber." Eyes wide, he just stared. "She does _not_ like to be kept waiting." He nodded and followed the Wraith to a large room where a female with short dark hair awaited him.

When he finally chanced a glance at her, she'd turned her piercing eyes on him. The creature that had once been Rodney McKay bowed. "You sent for me, my queen?"

~~O~~

John carried his children into the kitchen where his wife was making dinner. "We missed you, daddy." His daughter told him as he squatted to set her and her brother on the floor.

"I missed you guys too, pipsqueak. Every single day." He reached out and tickled her in the ribs making her giggle.

"24/7?" the boy asked.

"You bet!"

A pair of sneakered feet came into his line of vision. As he stood, his eyes trailed up a pair of shapely legs, white shorts and past a green T-shirt until he was gazing into hazel eyes surrounded by honey blonde hair tied back in a ponytail. Eyes that looked at him with such affection it always made his heart skip a beat.

Her hands framed his face as she kissed him. He kissed her back, his hands coming to rest on her waist. When they parted, their foreheads touched in the ritual greeting they'd taken from the Athosians.

John looked down when his son tugged on his uniform jacket. "Daddy, mommy has a surprise for you."

"Oh? What's the surprise, mommy?"

Amanda's eyes glistened with unshed tears. "Why don't you and your sister tell him?" John Rodney and Caroline Elizabeth came to stand in front of their mother. "On three, guys. One…two…_three!_"

"We're havin' a baby! Yay!"

After a stunned moment of silence, John whooped for joy too, picked his wife up and spun her around. Their lips met again as he set her back on her feet. "_Oh,_ Mandy."

~~O~~

Jennifer had fallen asleep outside the brig watching Rodney sleep, a portable scanner held in her right hand. He'd been asleep for more than ten hours, compared to almost none in the previous thirty-six. But it wasn't at all strange for him to do so. He loved to sleep but he also loved to work, two situations that were frequently at odds with each other.

The sound of footsteps woke her, bringing her to her feet as Teyla and Ronon joined her.

Keeping her voice low, Teyla smiled gently at Jennifer. "How is he?"

"About the same as when you were here before. He's called out a few times. Must've been having one _hell_ of a dream."

Remembering the one she'd had a few nights ago, Teyla smiled humorlessly. "Unfortunately, I don't have to imagine. Perhaps we should leave you to rest."

"No, it's fine. I was just about to wake him, see if he's ready to eat."

Teyla turned her head to the side as if listening to something only she could hear. "That won't be necessary. He's waking up."

Rodney began moaning, his legs twitching as if he were running from something or someone. Jennifer stepped as close to the forcefield as she could without being stung. "Dinner time, Rodney."

He ignored her, his wriggling turning into thrashing. Jennifer lifted a hand to call for assistance but stayed her hand when Rodney rolled over, revealing his face. A gasp came from both Jennifer and Teyla.

The physicist's short brown hair had begun to turn white and the skin of his face had taken on a pale cast. His head rolled side to side, his eyes fluttering open. He sat up then stood. Looking first at Jennifer and Ronon, he didn't appear to recognize them. His head kept turning until he saw Teyla. He dropped his eyes submissively and when he spoke, his voice was a raspy tone as if he needed to gargle or clear his throat.

"I am at your service…my queen."

~~O~~

Carson watched Amanda sitting at John's bedside holding his hand. She'd spent nearly every spare moment in the exact same place since he'd gone into the coma. Sometimes she talked to him, telling him about her day, their progress on finding a cure, funny things that happened, anything to get through to him and keep him anchored in this world. Who knew if it helped or not? But it couldn't hurt and it made those left behind feel as if they were doing more.

The hand she held squeezed and released hers over and over. Though it seemed as if he were reacting to what was going on around him, they couldn't be sure.

He laid a hand on her shoulder, giving it a small squeeze. She looked up with a smile. "Love, why don't ya go get something to eat, maybe rest a wee bit? I promise t' give ya a call if there's any change."

Amanda nodded. "Not a bad idea. Why are the chairs in here so uncomfortable? My back hurts." She gave him a hug before leaving.

Carson checked John's vitals noting that his EEG readings had changed. Not much, but enough to make it noteworthy. "I wonder what you're thinkin' about, John. Surfin' some unspoiled planet? Fightin' the Wraith? Makin' love? Whatever it is, it's registering here in the real world so keep at it, m'boy."

~~O~~

Jennifer tried not to panic. To Teyla and Ronon, she said, "He _can't_ have made a complete change in so short a time."

"He has not. Rodney is still inside. We only need to find him."

The medical doctor moved close to the forcefield again. "Rodney!"

The eyes that were still blue blinked several times then closed, his hand coming up to press against his forehead. He shook his head as if to clear away the cobwebs. When he opened his eyes again, he looked right at Jennifer then Teyla and Ronon. "Why are you all _staring_ at me? Do I have something between my…" He suddenly realized where he was. "What the _hell_ am I doing in the _brig_?"

Jennifer sagged with relief. "Thank goodness. How do you feel?" He seemed to be *her* Rodney once again.

"Um…hungry?" He did an internal diagnostic. "Yes, definitely hungry. I haven't eaten since…wait. Why am I in the brig?"

"It's a long story, honey and you probably won't believe me."

"Of _course_ I will." His tone left no doubt that he disagreed with her on this point.

Teyla smiled and gave Jennifer's arm a squeeze. "I will bring him something to eat."

At her retreating back, he shouted, "No citrus. I'm allergic!"

~~O~~

John reached the driveway of his home several steps behind his teenaged son. Both were sweat-soaked and panting, John much harder than the boy.

"Beat ya again, dad!" The young man raised his arms in the air and ran triumphant circles around his father. "Woohoo! I'm king o' the galaxy!" His voice had changed recently. Now it was deep with an odd reverberating quality.

"Don't get cocky, kid."

They both turned when the front door opened and Amanda came out, a bottle of water in her hand. "You're getting forgetful in your old age, John." He snorted, opened the bottle and took a long drink as his wife turned to their son. "And you, young man, go get ready for dinner while I talk to your dad."

"Yes, my queen." He said mockingly, brushing his long white hair out of his face and winking one yellow eye.

Just as he reached the front door, Amanda shouted, "Todd, tell your sister to set the table."

"Sammy! Mom said to set the tab-" The door slammed on the last syllable.

When Amanda faced him again, John was staring after the boy, his what-the-hell expression in place. "His _name_ is _Todd_? Why the _hell_ would I name one of my kids after a _Wraith_?"

She gave him a quick kiss. "It's never bothered you before. Why now?"

"Not sure." John followed her up the curved walk to the front porch of their two-story home. "There's something really, really _wrong_ with this picture."

~~O~~

"Dr. Beckett?" The young African-American doctor stood in the doorway of the lab where Carson was working. He carried a tablet and had a puzzled expression that was tempered by the slight smile that turned up the corners of his mouth.

"Come in, Cedric. What's that ya got there?"

"Something you need to see. This…" Cedric tapped a few keys on the tablet sending info to the monitor on the counter to the left of the microscope Carson was using, "…is Colonel Sheppard's EEG readings since he lapsed into the coma." He indicated several places where John's brain showed more activity than was normal in a comatose patient.

"I see. Huh." Carson pulled at his upper lip in thought.

Cedric pointed out the timestamps. "Each increase in brain activity coincides with someone talking to him while they change his IV, turn him over, shave or bathe him, whatever. To go by these readings, he _really_ appreciates the attention to detail."

Carson laughed with Cedric, lowering his voice to a whisper. "I'd wager that most of the men on base would enjoy having the likes of Marie, Sandy, Isabelle and Peri give 'em a sponge bath. For the rest of the fellas, we have Sonny."

"If anyone's listening, I have _nooo _comment. If not, I'm not ashamed to admit I'd be willing to spend a few days or even weeks in a coma _just_ to get the sponge baths." With a wicked grin, the younger man brought his attention to other more active areas. "And _these_ are the times Dr. Cole is talking to him, holding his hand, performing his physical therapy and what have you."

"It's triggered by direct physical contact between the two."

"Whatever it is, he _sure_ doesn't react that way to anyone else."

~~O~~

Teyla was in the brig area keeping watch over Rodney while Jennifer tended to the needs of her own body. Ronon frequently accompanied her but this time she was alone.

The physicist had demanded his computer so he could continue to work and Radek was more than happy to assist. The two of them would sit on opposite sides of the forcefield and speak in that language reserved for their profession. Until this last time.

Radek had come as he had been doing, seated himself on the floor and waited for Rodney to wake up. But Rodney had awakened in his Wraith persona. When in this state, the only person he would respond to was Teyla, whom he saw as his hive's queen. Ronon had been here but there was little he could do without going inside the enclosure.

Rodney had threatened to feed on the Czech and when that got little reaction, he'd thrown his computer at the forcefield smashing it to bits. When Ronon attempted to mediate by threatening both of them, he was ignored by Rodney as unimportant and therefore unworthy of being spoken to.

Movement within the enclosure drew Teyla's attention. Rodney was pacing the interior from one end to another. She'd already sensed his mind awakening but now it was different. Since shortly after the accident they'd been able to feel the presence of one another though it had been a sort of passive sense, just there. This was the first time his mind had ever actively sought hers out though he was nowhere near powerful enough to influence her actions as had the queen they'd encountered at the drilling station had done.

*My queen, have I displeased you in some way?*

**No, you have performed well**

*Then why am I a prisoner?*

**It is a part of my plan which will be revealed at a time of _my_ choosing. Until then you will remain as you are**

*Yes, my queen*

At this point, Rodney stopped moving, pressing his hands to his temples and rubbing. "That is _so_ weird. It's like having a dual personality only they both know about each other and neither one has full control." He seated himself on the bench with a heavy sigh. "Sometimes I wonder which is the real me."

Teyla walked to the edge of the enclosure. "Do not despair, Rodney. I'm certain a cure will be found for you _and_ for John."

He came to stand in front of her, his hands coming up as if to grasp the bars then dropping to his sides. "How is he?"

"Still in a coma, I fear. There is talk of putting him in stasis in order to prevent his condition from deteriorating."

"You know, this is going to sound petty, but it really _is_ his own fault. As long as I've known him, he's never learned that 'touch nothing' means _don't touch anything_. That's what he was doing when we first met. He ever tell you about that?"

"I do not believe so." Teyla smiled to herself. This was a perfect opportunity to keep Rodney grounded in this reality. "Please continue."

"He'd been assigned to fly General O'Neill to the secret base in Antarctica. While Elizabeth, Dr. Jackson, the General and I were having a meeting of the minds, John wondered around and ended up in the Chair Room with Carson…"

~~O~~

Marie called Carson away from John's bedside to show him the Colonel's latest round of tests. She didn't need to ask if it was bad news; she'd been a nurse long enough to know. If they didn't figure out something soon, the damage to his organs would be irreversible.

Jennifer entered with Amanda, both women in clean clothes that looked like they'd slept in them. They joined Carson while Marie moved over to check on a Lieutenant from AR-6 who'd dislocated his shoulder. He was an outrageous flirt who made her laugh as she cut up his chicken for him. Just as she finished, alarms began blaring sending her rushing away. "Doctors, he's coding! We have a Code Blue!"

**TBC**


	9. Mending a Torn Existence

**A/N:** As always, thanks to my brainstorming buddies ladygris and dwparsnip.

**Threads**

**Chapter 9**

**Mending a Torn Existence**

"Code Blue!"

Carson, Jennifer and Amanda were at Marie's side, already at work on the figure in the bed, doing what had to be done to save the man's life. A few minutes later they stepped back satisfied that their charge was stable once again.

"Monitor his vitals every fifteen minutes and have the usual tests done," Carson told Marie. The nurse nodded and bustled away. To Amanda and Jennifer, he said, "I'll keep an eye on Lieutenant Dobbs. You two go take care of John and Rodney."

"Thanks, Carson." Both women gave the Scot a tight hug before Amanda went to John's bedside and Jennifer to the brig.

~~O~~

_John walked aimlessly through the halls of Atlantis, his mind and body numb. When he finally became aware of his surroundings, he was in front of the quarters he shared with his family. Only now his family was about to be devastated._

_Team Sheppard and AR-3 had been the escorts of a medical team that had traveled to M10-992 to treat an outbreak of a flu-like illness. There were no deaths from the disease among the residents but while there, the Wraith had come. _

_They'd gotten as many as possible into the caves north of the village but about twenty had been culled including his wife. The rescue only encountered one hitch. When they found Amanda, she was being fed upon. He'd killed the Wraith before he could take all of her life but it was too late. _

_She'd been brought back to Atlantis and had died within the hour leaving him a single father with two small children. How he was going to tell them their mother wasn't coming back, he had no idea. Passing his hand over the bioscanner, he entered the brightly lit main living area. The voices of his children could be heard talking and laughing with Aylanna, the Athosian woman who watched them occasionally._

_Unhooking his weapon from the neck strap, John pulled off his vest, opened the cabinet next to the desk, shoved both inside and locked it. Somehow he made it to the sofa without falling down or tripping on one of the toys the kids routinely left strewn across the floor. Now that he was alone, the tears he'd held back stung his eyes just as Jonathan and Elizabeth came running in to throw themselves into his arms. He hugged them close, not wanting to let go._

"_Daddy! We missed you!" His son had both arms around his neck. Over the boy's head, he nodded to Aylanna and she quietly slipped out._

"_Missed you, too, squirt." This wouldn't get any easier so he took a deep breath and had them sit on the sofa while he crouched in front of them. "Johnny, Lizzi, I've got something to tell you."_

_His daughter suddenly realized someone was missing. "Where's mommy? She said she'd be home in time for dinner. I gotta go to ballet class tonight and she's 'sposed to bring cookies."_

"_That's what I have to tell you. Mommy…won't be coming home tonight."_

"_Did she get stuck workin' again?"_

"_No. Not this time. You see, there was, well, sort of an accident while mommy was working…"_

Forty-five years later and John could still remember that night as if it had just happened. The three of them had slept in his big bed together holding each other and crying until they fell asleep.

Using a cane to steady himself, John made his way into the living room of the home he'd lived in since retiring from the Air Force almost twenty years before. On the walls were photos of his and Amanda's children, grandchildren and great-grandchildren. It made him sad that she hadn't been around to see the beautiful family they'd created together.

With a snort, he imagined what she might have said and done when their daughter, Lizzi, announced that she was getting married…to Rodney and Jennifer McKay's son William. She would have been so happy that she'd have started planning the wedding right that very minute never once thinking about what it would be like for her husband to be in-laws with the self-professed smartest man in two galaxies.

With a groan, he sat down in his favorite recliner and thought the vid screen to life. He retrieved a beer from the 'fridge unit kept next to the chair and settled back to watch his alma mater play against Arizona State in the championship game. He had a running bet each season with his long-time friend, Evan Lorne, a graduate of ASU, on which team would be the big winner.

Halftime came up and he thought about getting a snack but remembered he was out of popcorn. Instead, he took a drink of beer and closed his eyes trusting that he'd wake up when the third quarter started. The hand that held the bottle slid off the arm of the chair and a few minutes later, his fingers went lax. The bottle fell, spilling the remainder of its contents into the carpet.

Standing in front of the vid screen watching the last bit of life drain out of his worn body, he was startled when someone spoke to him.

"John."

Turning quickly, his eyes widened in shock when he saw the figure of his wife standing before him dresses in her Atlantis uniform as he'd last seen her. Not trusting his eyes, he reached out to touch her face with his fingertips. "Amanda? Is-is it really…you?'

"Of course, my love."

Suddenly he felt…different. All the aches and pains he'd lived with for decades were gone. Looking down at himself, he found that he once again looked as he had when he and Amanda had first been married, they both did. With a whoop of joy, he picked her up and spun around. She slid down the front of his body, her lips attacking his hungrily. Pulling away, he touched his forehead to hers. "Oh, _Mandy_."

~~O~~

In the Infirmary, alarms blared, sending Carson running to join Amanda at John's side. His vital signs were erratic. They returned to normal within a few minutes, but it was happening with greater frequency. Carson had already made the arrangements, now it was time. If they didn't put John is stasis _now_, there was a very good chance he wouldn't make it another forty-eight hours.

~~O~~

Jennifer arrived in the brig to find Teyla looking annoyed and she didn't have far to go to find the source. Rodney was sitting on the padded bench with his arms crossed, a food tray and its former contents strewn across the floor mixing with the bits and pieces of the shattered laptop.

"What's going on?"

Teyla took Jennifer to a far corner. "He is…upset that we will not allow him to leave. He has also spent more time in his Wraith persona than as himself these last few hours. I fear we will completely lose him if something isn't done soon."

"I didn't want to do this but he'll be better off if he goes into stasis." Jennifer moved away to make the arrangements.

~~O~~

"We have to risk it, Carson. John needs to know what's at stake." Amanda kept her voice level and her expression neutral even though she knew Carson would see through it.

"Aye, you're right. But we'll do it once we get to the stasis chamber just in case." He signaled and medics helped him push the bed holding Atlantis' comatose military commander. They exited the bulk transporter and guided the unwieldy bed down the hall slowing to avoid the junk they hadn't bothered to remove in the years since they'd been in the city. Carson took out a prefilled syringe, inserted it into the port in John's IV. It may have been Amanda's imagination, but it seemed liked he'd hesitated just a fraction of a second before pressing the plunger.

On the monitor, John's vital signs slowly improved as he began to moan and turn his head side to side. His right arm covered in dark hair resting on his stomach slid up over his chest to take hold of the oxygen mask over his face and pull it down under his chin. His mouth moved but his voice was so soft they couldn't hear.

Carson leaned close. "What's that yer sayin', John?" He listened for a moment, his face dissolving into a smile as he chuckled lightly.

"What did he say?" Amanda wanted to know.

"He said, 'Quick, Robin! To the Batpoles!'" Everyone laughed because they all knew of his affinity for the original Caped Crusader series.

The laughter further roused John. He looked around and dropped his head back to the pillow. "This doesn't look like the Batcave."

"No, it's not." Carson's smile was gone now as the reason for coming to this place reasserted itself. "We're at the stasis chambers."

"Somebody dyin'?"

"Afraid so."

John's eyes drooped closed again. "McKay?"

Amanda put a hand on Carson's arm, her eyes asking him to let her speak. "Hey."

John's smile at seeing her changed to a frown. "Oh, crap. I didn't do somethin' uncivilized durin' our date, did I?"

"No, of course not." Her eyes asked the others for privacy and they moved a discrete distance away from the couple. "John, you've been in a coma for the last few days. Our most recent tests and scans show…" Her eyes began to sting as tears threatened. "The ATA gene was…it was sort of the thread that kept your DNA together. Now that it's gone, you're…unraveling."

"So McKay's okay?"

Amanda smiled. It was so like John to be more concerned for his friend than himself. "No, he's not, but we're working on it. Right now, our top priority is keeping _you_ alive long enough to figure out a cure. That's why we're in the stasis room. We need to put you on ice for a few days, a week at most. Will you give your permission for us to do that?"

"After seven hundred years, a week'll be a cakewalk. Two conditions." John held up three fingers, dropping his voice to a whisper. "Let's lose the catheter and get me some friggin' _pants_!"

~~O~~

A nurse and medic came in to see to John's requests then moved the bed around so it would be a shorter walk for him. He swung his legs over the side and pushed off, his knees buckling the second his feet touched the floor. Carson and Amanda held him up until he was able to stand on his own staying with him until he'd stepped into the pod.

"I knew you'd want this." Amanda reached into her pocket and pulled out his black wristband. "Someday you'll have to tell me why you wear it."

"Thanks." His eyes locked with hers as he slipped it on.

Over her shoulder, Amanda said, "Carson, could you give us a second." The Scot nodded and went to stand next to Radek. She gestured and the Czech handed her the pod control.

"Well, I guess this is it. See you in a few days."

"John, there's something I have to say, something I should've said long ago."

"Maybe, uh…" his eyes widened in surprise as she leaned forward and whispered in his ear. Before he could respond, she stepped back and activated the stasis pod leaving him staring sightlessly out at her with that same stunned expression.

~~O~~

"You don't need _guards_, Jennifer. I'm not going to make trouble." Rodney tried to use his most reasonable tone. Trouble was he used sarcasm and mockery so much in his daily life that it was difficult for him to change. The guards said nothing, just kept a wary eye on their charge as Jennifer, Teyla and Ronon following along behind.

"Sorry, Rodney. Major Lorne's orders."

They entered the hall near the stasis chambers just after the medical team returned over the same path. As they made the left turn that led to their destination, Rodney stopped cold, swaying as if dizzy. The guard just behind him whipped out his stunner and took a step back.

Jennifer started forward but Teyla stopped her with a hand on her arm. She didn't need to say anything. The look in her eyes was enough. He was changing again.

Rodney's head came up glaring at the guards. Without a word, he leapt on the Marine Sergeant to his left and the other two joined in. Growling deep in his throat, he grappled with the three men who were doing their best to restrain the scientist without injuring him. He shouted threats and promised dire consequences for all if he wasn't released.

Suddenly, Teyla pushed through to Rodney's side. "Stop this immediately!"

At the sound of her voice, Rodney did as she commanded. "My queen, how can you allow this?"

She gave barely a glance at the startled faces of the soldiers as they let go of Rodney's arms. "It is part of my plan. Accompany them to the chamber or _you_ will be the main course the next time I feed."

His eyes dropped to the floor obediently. "Yes, my queen." True to his word, he made no further attempts to escape and went meekly into the prepared stasis pod.

Jennifer took a deep breath and hit the activation sequence.

~~O~~

Later that night, Jennifer went back to the stasis room to check on Rodney. A small sound drew her to where Amanda was sitting on the floor. She knew her 2IC would be here and she'd come prepared. Dropping down next to Amanda, she passed her a bottle of beer. Without a word, they sat there together drinking beer and keeping watch.

**TBC**


	10. A Warm Blanket on a Cold Night

**A/N:** I want to thank ladygris for all her help with this story. She's been a great sounding board and a well-spring of ideas.

Next I would like to thank dwparsnip for his contribution to this chapter. John's comment when coming out of stasis was his idea.

~ Sandy

**Threads**

**Chapter 10**

**A Warm Blanket on a Cold Night**

Radek looked up from his workstation when Woolsey, Evan, Amanda, Jennifer and Carson came in. "Thank you for coming. I have good news. There _is_ a way to cure Colonel Sheppard and Rodney."

"Great. How do we do that?" Evan was more than ready to get this all over with. He'd been back and forth to M7M-536 several times a day checking up on the patrols. With that, and all the other duties he'd taken on while Sheppard was out of commission, he was ready for a little R&R.

"Oh, well, it's extremely complicated but with what little help Rodney was able to provide, we, the rest of the staff and I, with the contributions from the medical staff, have been able to work out a solution. See…" he turned his monitor so they could see it, "…first we have to…"

"Yes, that's very interesting, Radek, but none of us understands even a portion of what you're showing us so we'll just take your word for it." Jennifer told the physicist.

"Of course. The most important thing you need to know is we _must_ reverse the genetic changes within the next seventy-two hours or there will be no way to save them."

~~O~~

Carson and Amanda helped John step down from the stasis pod to the wheelchair waiting to take him to the Jumper Bay for the trip back to M7M-536. She draped a blanket over his lap before pushing him in the direction of the transporter where Carson waited for them. He started shifting making the chair swerve.

Amanda looked over his shoulder to see him with one hand under the blanket feeling around. At least she _hoped_ that's what he was doing. Finally she leaned down next to his ear. "John, what are you _doing_?"

Startled that he'd been caught, he snatched his hand out guiltily. After glancing around to make sure no one else can hear, he whispered back, "I'm just making sure…everything's the same as it was when I went in." At her perplexed look he added, "Cold is NOT a guy's best friend."

Amanda couldn't help smiling. "I'm sure everything will be back to normal very shortly."

John grumbled. "Do _not_ use the word 'shortly' around a guy just out of the deep freeze."

~~O~~

When the others had gone, Jennifer, Ronon, Teyla and a squad of Marines, led by Gunnery Sergeant Brackman, stood ready to bring Rodney out of stasis.

"Keep your weapons holstered but stand ready just in case." The Sergeant scowled at Ronon when he heard the big guy's energy pistol power up. Ronon just looked back.

Jennifer touched the controls and Rodney was released from stasis. Two Marines stepped forward and caught him as the field dispersed and he fell out of the pod. Before he could say a word, the standard prisoner's arm and leg chains were snapped around his wrists and ankles. And he wasn't happy about it.

"You know, you _really_ need to work on your people skills." Rodney jangled the chains and sighed in acceptance. "Can we at least take the back way? Being seen like this won't do much for my rep as one of the cool crowd."

Jennifer rolled her eyes and started walking. "You sound like Sheppard. Let's get going before something else happens."

After casting a glance over his shoulder at the Marine detail, he moved up to walk at her side. "You found a cure? That's great!"

"Actually, Radek and Carson figured it out." At Rodney's horrified look, she added, "Oh, with your help, of course."

"Naturally." He wanted to put his arm around Jennifer's shoulders but the chains prevented him from doing so. Though that didn't bother him as much as her stiffening when he tried to touch her hand. "Um, how's John?"

"He was already in stasis when we brought you down."

Teyla was on Rodney's other side. "Yes. You reverted just as we arrived."

"Oh. Sorry. How did you…"

The Athosian smiled ruefully. "Your Wraith persona is quite compliant when given orders. I must confess that I find it very…satisfying."

Before Rodney could formulate a reply, he stumbled to a halt, both hands coming up to rub his temples. His eyes opened again looking at Teyla and ignoring everyone else. "What is happening?"

She knew what was coming before he did and was prepared with an answer. "My plan is ready to be executed. I will let you know when it is time to act."

"Yes, my queen."

~~O~~

Evan landed the Jumper as close to the lab as he could because Sheppard refused to be pushed in a chair and had even less interest in being carried. The Jumper was cloaked and Evan contacted the patrols, receiving negative Wraith sightings.

On the flight from the Stargate, Rodney had gone back to being himself again for which they were all thankful. Now all they had to do was get inside and put their plan into action.

Ronon and Evan stayed by John's side throughout the walk to the lab. A few meters inside, John's legs gave out and amid protests Ronon scooped him up and carried him the rest of the way, depositing him on his feet again when they reached the lab where it had all started.

While Radek set up the equipment, Rodney stuck his hands out as far as he could with the restraints on. "As fashion-forward as it is, can we lose the jewelry, Sergeant?"

"Of course, doctor. And call me Gunny. Everyone does. Even my pop."

"Well, I wouldn't want to go against such a long-standing tradition, Gunny." He rubbed his wrists and went to stand next to Radek as he readied the program.

John looked over the Czech's other shoulder. "So how's this gonna work, doc?"

"Basically, you and Rodney will go back into the device in the opposite positions that you went in originally."

Rodney face took on an alarmed expression. "Is it gonna, you know, hurt?"

"Uh, there will be some discomfort." The physicist sagged in relief until Radek continued, "By 'some' I mean 'a great deal' and by 'discomfort' I mean 'pain like you have never before experienced.' All of the muscles in your extremities and around your torso will contract repeatedly such as when you have a cramp."

John winced. "That's what happened to _me_. It _hurt!_"

"Yes. But it is the only way. I have programed the device to…"

Waving away the explanation, Rodney asked, "Can we just get _on_ with it? Please?"

~~O~~

Jennifer came to Rodney's side, a portable scanner in one hand. She started to reach for his hand to comfort him as she always did but dropped it to her side. Her love for him was as great as it ever was. She just couldn't put aside the memory of the night he'd almost assaulted her. He hadn't been in control of his actions, and she knew that, however it didn't stop her from being afraid of him. Instead, she rubbed the wrist of the hand holding the scanner. Except for one, the bruises were nearly gone though the memory lingered. She filed it away for another time. Right now, John and Rodney needed her full attention.

~~O~~

"Okay. We are ready." Radek led the two men over to the device. "Rodney, you will stand where Colonel Sheppard was the first time and Colonel Sheppard will stand as you were that day." He waited while they complied. "Now you will need to, uh, hold hands."

"_What_?" Rodney and John exclaimed at the same time.

"According to the mission reports, the two of you were touching when the device was activated, so you must touch now."

"Oh. Okay." John acquiesced extending his right hand. "I'll hold hands on the first date but you're _not_ getting a good-night kiss."

"I'm sure Rodney'll forgive you." Jennifer responded with a tongue-in-cheek smile and stepped over to the main console.

Rodney finally took John's hand and signaled to Radek they were ready. The Czech reached past them to use the keypad that had been the cause of all their problems. "When I say now, touch this…" he pointed out the correct key then moved back over next to Jennifer. The Marines, Carson, Jennifer, Amanda, Ronon and the medics that had accompanied them took several steps back. Radek saw and smiled. "The field will not extend more than a few centimeters beyond the control pads on the floor."

"Maybe." Carson agreed. "But it's better to be safe than sterile, _I_ say."

Radek had no argument for that and continued with his work.

Teyla inhaled sharply, her eyes widening in alarm. She took a step forward only to be stopped by Brackman. "Hurry, Radek! He is reverting again."

The Marines raised their stunners, training them on Rodney just as he began to sway, his free hand pressed to his forehead.

"Now, Rodney!"

But it was too late. Rodney's left hand tightened its grip on John's while his right came up. The fingers curled in toward the palm then out again. When Rodney lifted his head again John could see the intent in his eyes. If he were fully Wraith, the Colonel would be his next meal. Mentally crossing his fingers, John wrapped both arms around Rodney then reached past him to activate the device. He closed his eyes and waited for the pain.

~~O~~

John opened his eyes to one of the most beautiful sights he'd ever seen. He was on his back with Amanda kneeling next to him, scanner in one hand and her professional mask in place. At least until she smiled. It made her eyes sparkle. "Contact. He's awake."

"Colonel, how do you feel?"

Turning his head, John scowled at Radek as he and Amanda helped him sit up. "You didn't say _anything_ about passing out."

"I didn't _know_."

John groaned as he was helped to his feet. Once upright, he realized he felt stronger than he had since this started. "How's McKay?"

Jennifer and Carson were kneeling beside the physicist who was curled up in a ball. John winced again remembering how much it had hurt. A few minutes later, Rodney began to stir then to groan. "Son of a _bitch_ that hurt!"

"Can you stand, Rodney?"

"My entire _body_ feels like I've been beaten and left for dead. What makes you think I can _stand_?"

Carson signaled Gunny over and together they helped Rodney to his feet. "How about something for pain?" He circled each arm, grimacing with each movement.

Jennifer shook her head. "Not until we do a few tests." She reached into one of the many cases filled with equipment and removed a portable DNA scanner. Looking from one to the other, she asked, "Okay, who wants to go first?"

John and Rodney pointed at each other and said, "He does."

Amanda came to stand at Jennifer's side. "John wants to go first." She peered into the Colonel's eyes. "Right?"

"Fine. I'll go first. What do you need? Blood? Spit?" The two women exchanged a smirk. "Aw, come _on_." He leaned close lowering his voice. "You really expect me to, you know, _here_?"

"We're _kidding_, John. We'll do that test when we get back to Atlantis." Amanda pulled out a large swab. "Open." He did as she asked and watched while she used the specimen to start the test. Out the corner of her eye, she watched as John began to pace from one side of the room to the other. The next time he came near she handed him a bottle of water. He gave her a smile of thanks but didn't say anything. A few minutes later the scanner beeped. Amanda read the results then showed them to Jennifer and Carson.

John looked from one to the other waiting for someone to say something. "Well?" For an answer Carson picked up an LSD and tossed it to John who caught it automatically. He held it face down, took a deep breath and turned it over. It lit up, blips on the screen showing the entire team. "It works! Does this mean…"

Clapping John on the shoulder, Carson finally let a big smile come to his lips. "It means you are one hundred percent John Sheppard…again."

"Congratulations, sir." Evan said from his place at the entrance.

"Thanks, Major. By the way, I'm in the pilot's seat on the way back."

Evan nodded once. "Wouldn't have it any other way, Colonel."

"What about _me_?" Rodney hated being left out.

Jennifer used another large swab to take Rodney's specimen and performed the same test Amanda had done for John. When the results came, she showed them to Amanda and Carson. "He's Rodney again."

"I'm not gonna change into a Wraith anymore?"

"Of course not, Rodney." Carson told him gently. "And Radek was able to program this blasted thing to allow you to keep the natural ATA gene but there's a rub."

Now John was interested. "Rub? What're you talking about?"

Jennifer came to stand in front of the two men, her eyes on Rodney's face. "The only way we could allow you to keep the natural ATA is if you also retained a small amount of _John's_ DNA." She looked from one to the other waiting for a reaction.

Rodney and John looked back at her for a while thinking it over then exchanged a what-do-_you_-think expression. They both shrugged and looked at her again, speaking at the same time. "I can live with that."

~~O~~

The radio crackled. "Billig to Lorne. Someone's dialing in."

John moved to his second's side. "One guess who it is."

"Wraith." Evan answered without a pause. "Do _not_ engage." A double click was the only response. "All units, copy?" Within a few seconds he received affirmative replies from his people.

"Pack it up!" John ordered, very glad to be back in charge again. "We're getting out of here."

Reaching into his backpack, Evan pulled out a P-90 and passed it to his CO.

John acknowledged it with a nod as Evan passed him extra mags. He also silently thanked Amanda for helping him get into his uniform before they left on this very odd mission. At least he wouldn't be fighting the enemy in what amounted to pajamas. He checked his weapon, set it to automatic and led the way to the exit. "Ronon, you're on point with me. Lorne, you and Brackman on our six. Docs, you're in the middle. Just do _what_ you're told _when_ you're told and we'll get out of this with our asses intact."

Though John would never say so out loud, having friends who were as close as family was like a warm blanket on a cold winter night. It made him feel as if the icy wall he kept around his heart had melted just a little.

~~O~~

Crouched back to back in a thick stand of bushes, John and Evan watched several Wraith pass their hiding place. When they were out of range Evan whispered over his shoulder. "We don't _have_ to fight them unless you really want to."

"Oh?"

With a smug grin, Evan told him, "The entire facility is wired with C4 set to blow when you give the word, sir."

"_That's_ what I like about having you on my team. You always give the perfect gift." John clicked the radio in a pre-arranged signal and waited until they'd received the signal that everyone but themselves had fallen back to the Jumper.

Reaching into his vest pocket, Evan produced the detonator. "Would you like the honor, sir?"

John grinned, snatched it from his hand and clicked the radio one more time. "Fire in the hole!" He flipped up the guard and pressed the button. A series of explosions rocked the area and sent both men running for better cover as hot chunks of the building rained down around them. They jumped back when the head of a Wraith landed in front of them. John didn't know if he was glad or sorry it wasn't Todd. Once they were at a safe distance, they stood watching the Wraith lab burning bright orange in the distance. "That _never_ gets old."

"No, sir," Evan agreed with his CO.

Hefting his P-90, John clapped Evan on the shoulder. "Come on. Let's go home."

~~O~~

After dinner, Rodney walked Jennifer back to her quarters. At her door, he leaned down to kiss her. It was quick, just a slight pressing of their lips together. As always, her touch reminded him how much he loved her. Taking another step forward, he let his hands lightly rub her upper arms as he tilted his head to the side to deepen the kiss.

She stiffened, turning her head away and stepping back so that his hands fell to his sides. "Jennifer, is something wrong?"

"It-It's nothing. I'm just tired and you need to rest." She gave him a quick peck on the cheek and went into her room.

Rodney stood looking at her door long after it closed. With a heavy sigh, he continued around the corner to his own room and got into his pajamas. He lay down on the bed, his hands laced together over his stomach, the thumbs twirling first one way then the other. Rolling onto his side, he pulled the sheet and blanket over himself, hugging the pillow that still retained Jennifer's scent. Recent events took their toll and he was soon asleep.

~~O~~

Inside her room, Jennifer stood in the dark, a tear forming, welling up until it rolled slowly down her cheek. Brushing at it angrily, she went into the bathroom to change for bed. When she returned to the bedroom, she climbed under the covers and rolled onto her side but couldn't relax. She could still smell Rodney on the extra pillow. Normally she'd cuddle the pillow when she wasn't able to cuddle him but couldn't get the picture of his face the night he nearly assaulted her out of her mind. She shoved the pillow into the closet, crawled back in bed, shut off the light, pulled the covers up to her neck and tried to go to sleep.

~~O~~

John had been released from the Infirmary to light duty then to full duty making it almost three weeks since they'd returned from M7M-536. Though Amanda had seen him every day when he came in for his mandatory check-up and had dinner with him and his team on several occasions, he never mentioned what she'd said to him just before he'd gone into stasis. This brought three possible scenarios to mind. One, he didn't remember. Two, he didn't feel the same. Three, he was waiting for the right moment to bring it up. She held onto the hope that it was the third and tried to be patient. However, even Job had his limits and her endurance was nowhere near as strong. If he didn't say something soon…

The chime announced a visitor at her door and when she opened it, there stood the man who'd occupied her every waking thought since before the accident. Yes, she'd finally admitted to herself that she was in love with her college pal and had been for a while.

He was in his black mission uniform, the sleeves rolled up to his elbows. It made him look strong and heroic, though she'd never tell him so. He leaned his shoulder casually on the doorjamb, hands in his pockets.

"John."

"May I come in?"

She stood back so he could enter.

John glanced around her room taking in the photos and knick-knacks and the quilt her grandmother had made for her the year she passed away. She thought he'd laugh at the stuffed animals on her bed but he didn't.

His hazel eyes landed on her again staring at her for so long without saying anything she had to clamp down on the urge to fidget. "Something I can do for you?"

"I'm here because…" his stance was relaxed, arms casually crossed, "…we have to talk."

"Oh? What about?" _Don't be coy! You __know__ why he's here._

"About what you said just before I went into stasis." John's arms dropped to his sides as he moved close enough to take her in his arms if he wanted to and he looked like he wanted to. "Did you mean it?" His eyes searched her face.

Amanda let her eyes meet his without flinching. "Yes."

"Good."

The next thing she knew, she was in his arms and he was kissing her as if he couldn't get enough. It went on for a while, never going beyond kissing and hugging. At least, not yet. Pulling away, he rested his forehead against hers, their warm breaths mingling between them. "Oh, Mandy."

**The End**

**A/N:** "Mandy," originally titled "Brandy," is a song jointly written and composed by Scott English and Richard Kerr. "Brandy" had been a hit in 1971 for Scott English in the UK and in 1972 for Bunny Walters in New Zealand. But the song was made famous by Barry Manilow in 1974 when he changed the title to "Mandy" to avoid confusion with Looking Glass's "Brandy (You're A Fine Girl)." His version reached the top of the US Hot 100 Singles Chart.

Yes, I know I've left some loose ends in this story but never fear. There's a sequel in the works that will tie it all up. At the moment, all I have is a tentative title: Threads II.


End file.
